US analysts knew Afghan site was hospital

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President Obama Apologizes for Afghanistan Hospital Bombing

WASHINGTON (AP) — American special operations analysts were gathering intelligence on an Afghan hospital days before it was destroyed by a U.S. military attack because they believed it was being used by a Pakistani operative to coordinate Taliban activity, The Associated Press has learned.

It's unclear whether commanders who unleashed the AC-130 gunship on the hospital — killing at least 22 patients and hospital staff — were aware that the site was a hospital or knew about the allegations of possible enemy activity. The Pentagon initially said the attack was to protect U.S. troops engaged in a firefight and has since said it was a mistake.

SEE MORE: U.S. says it conducted air strike near Afghan hospital

The special operations analysts had assembled a dossier that included maps with the hospital circled, along with indications that intelligence agencies were tracking the location of the Pakistani operative and activity reports based on overhead surveillance, according to a former intelligence official familiar with the material. The intelligence suggested the hospital was being used as a Taliban command and control center and may have housed heavy weapons.

After the attack — which came amidst a battle to retake the northern Afghan city of Kunduz from the Taliban — some U.S. analysts assessed that the strike had been justified, the former officer says. They concluded that the Pakistani, believed to have been working for his country's Inter-Service Intelligence directorate, had been killed.

Click through to see the fallout from the fatal bombing:

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U.S. airstrike on Doctors Without Borders hospital in Afghanistan
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US analysts knew Afghan site was hospital
FILE - In this Oct. 16, 2015, file photo, an employee of Doctors Without Borders stands inside the charred remains of their hospital after it was hit by a U.S. airstrike in Kunduz, Afghanistan. Russian airstrikes have reportedly hit at least a half dozen medical facilities in Syria, according to activists. In Yemen, an airstrike by the Saudi-led coalition hit a hospital run by Doctors Without Borders. Still, apart from rights groups condemnations, thereÂs been little international outcry, in contrast to a U.S. strike on a hospital in Afghanistan that killed 30 people. (Najim Rahim via AP, File)
The Doctors Without Borders hospital is seen in flames, after explosions in the northern Afghan city of Kunduz, Saturday, Oct. 3, 2015. Doctors Without Borders announced that the death toll from the bombing of the group's Kunduz hospital compound has risen to at least 16, including 3 children and that tens are missing after the explosions that may have been caused by a U.S. airstrike. In a statement, the international charity said the "sustained bombing" took place at 2:10 a.m. (21:40 GMT). Afghan forces backed by U.S. airstrikes have been fighting to dislodge Taliban insurgents who overran Kunduz on Monday. (Médecins Sans Frontières via AP)
The Doctors Without Borders trauma center is seen in flames, after an explosion near their hospital in the northern Afghan city of Kunduz . Doctors Without Borders announced that the death toll from the bombing of the group's Kunduz hospital compound has risen to at least 16, including 3 children and that tens are missing after the explosions that may have been caused by a U.S. airstrike. In a statement, the international charity said the "sustained bombing" took place at 2:10 a.m. (2140 GMT). Afghan forces backed by U.S. airstrikes have been fighting to dislodge Taliban insurgents who overran Kunduz on Monday. (Médecins Sans Frontières via AP)
The Doctors Without Borders trauma center is seen in flames, after an explosion near their hospital in the northern Afghan city of Kunduz . Doctors Without Borders announced that the death toll from the bombing of the group's Kunduz hospital compound has risen to at least 16, including 3 children and that tens are missing after the explosions that may have been caused by a U.S. airstrike. In a statement, the international charity said the "sustained bombing" took place at 2:10 a.m. (2140 GMT). Afghan forces backed by U.S. airstrikes have been fighting to dislodge Taliban insurgents who overran Kunduz on Monday. (Médecins Sans Frontières via AP)
In this Friday, Oct. 16, 2015 photo, the charred remains of the Doctors Without Borders hospital is seen after being hit by a U.S. airstrike in Kunduz, Afghanistan. Christopher Stokes, general director of Doctors Without Borders, which is also known by its French abbreviation MSF, whose hospital in northern Afghanistan was destroyed in a U.S. airstrike, says the Âextensive, quite precise destruction of the bombing raid casts doubt on American military assertions that it was a mistake. (Najim Rahim via AP)
In this Friday, Oct. 16, 2015 photo, the charred remains of the Doctors Without Borders hospital is seen after being hit by a U.S. airstrike in Kunduz, Afghanistan. The head of Doctors Without Borders, which is also known by its French abbreviation MSF whose hospital in northern Afghanistan was destroyed in a U.S. airstrike says the Âextensive, quite precise destruction of the bombing raid casts doubt on American military assertions that it was a mistake. (Najim Rahim via AP)
Afghan employees of a Doctors Without Borders hospital move debris of its damaged gate in Kunduz, Afghanistan, Thursday, Oct. 15, 2015. Taliban fighters took control of the key northern city late last month, leading to a protracted battle with Afghan forces supported by U.S. airstrikes. During the fighting, a U.S. air attack hit the hospital, killing at least 12 Doctors Without Borders staff and 10 patients. (AP Photo/Najim Rahim)
FILE - In this Oct. 16, 2015 file photo, the charred remains of the Doctors Without Borders hospital is seen after it was hit by a U.S. airstrike in Kunduz, Afghanistan. The Army Green Berets who called in the deadly strike on the Doctors without Borders trauma center in Afghanistan were aware it was a functioning hospital but believed it was under Taliban control, raising questions about whether the air strike violated international law.. (Najim Rahim via AP)
In this Wednesday, Oct. 14, 2015 photo, the charred remains of the Doctors Without Borders hospital is seen after being hit by a U.S. airstrike in Kunduz, Afghanistan. The attack, which killed a number of hospital staff and patients, was intended to back up Afghan forces fighting to dislodge Taliban insurgents who overran the strategic city earlier in the month. (Najim Rahim via AP)
In this Friday, Oct. 16, 2015 photo, an employee of the Doctors Without Borders walks inside the charred remains of their hospital after it was hit by a U.S. airstrike in Kunduz, Afghanistan. Christopher Stokes, general director of Doctors Without Borders, which is also known by its French abbreviation MSF, whose hospital in northern Afghanistan was destroyed in a U.S. airstrike, says the Âextensive, quite precise destruction of the bombing raid casts doubt on American military assertions that it was a mistake. (Najim Rahim via AP)
In this Friday, Oct. 16, 2015 photo, Christopher Stokes, the general director of the medical charity, Doctors Without Borders, which is also known by its French abbreviation MSF, stands near the charred remains of the organizations' hospital, after it was hit by a U.S. airstrike in Kunduz, Afghanistan. Stokes says the Âextensive, quite precise destruction of the bombing raid casts doubt on American military assertions that it was a mistake. (Najim Rahim via AP)
In this Friday, Oct. 16, 2015 photo, the charred remains of the Doctors Without Borders hospital is seen after being hit by a U.S. airstrike in Kunduz, Afghanistan. The head of Doctors Without Borders, which is also known by its French abbreviation MSF, whose hospital in northern Afghanistan was destroyed in a U.S. airstrike says the extensive, quite precise destruction of the bombing raid casts doubt on American military assertions that it was a mistake. (Najim Rahim via AP)
FILE -In this Oct. 14, 2015 file photo, the charred remains of the Doctors Without Borders hospital is seen after being hit by a U.S. airstrike in Kunduz, Afghanistan. The Army Green Berets who called in the deadly strike on the Doctors without Borders trauma center in Afghanistan were aware it was a functioning hospital but believed it was under Taliban control, raising questions about whether the air strike violated international law. (Najim Rahim via AP)
FILE -- In this Oct. 15, 2015 file photo, Christopher Stokes, the general director of medical charity Doctors Without Borders, which is also known by its French abbreviation MSF, stands at the gate of the organization's hospital, after it was hit by a U.S. airstrike in Kunduz, Afghanistan. Russian airstrikes have reportedly hit at least a half dozen medical facilities in Syria, according to activists. In Yemen, an airstrike by the Saudi-led coalition hit a hospital run by Doctors Without Borders. Still, apart from rights groups condemnations, theres been little international outcry, in contrast to a U.S. strike on a hospital in Afghanistan that killed 30 people. (Najim Rahim via AP, File)
Injured Doctors Without Borders staff are seen after an explosion near their hospital in the northern Afghan city of Kunduz, Saturday, Oct. 3, 2015. Doctors Without Borders announced that the death toll from the bombing of the group's Kunduz hospital compound has risen to at least 16, including 3 children and that tens are missing after the explosions that may have been caused by a U.S. airstrike. In a statement, the international charity said the "sustained bombing" took place at 2:10 a.m. (2140 GMT). Afghan forces backed by U.S. airstrikes have been fighting to dislodge Taliban insurgents who overran Kunduz on Monday. (Médecins Sans Frontières via AP)
U.S. Forces-Afghanistan Resolute Support Mission Commander Gen. John Campbell pauses as he testifies on Capitol Hill in Washington, Tuesday, Oct. 6, 2015, before the Senate Armed Services Committee hearing on the Situation in Afghanistan. U.S. forces attacked a hospital in northern Afghanistan last weekend, killing at least 22 people, despite "rigorous" U.S. military procedures designed to avoid such mistakes, the top commander of U.S. and allied forces in Afghanistan said Tuesday. (AP Photo/Carolyn Kaster)
The burnt Doctors Without Borders hospital is seen after an explosion in the northern Afghan city of Kunduz, Saturday, Oct. 3, 2015. Doctors Without Borders announced that the death toll from the bombing of the group's Kunduz hospital compound has risen to at least 16, including 3 children and that tens are missing after the explosions that may have been caused by a U.S. airstrike. In a statement, the international charity said the "sustained bombing" took place at 2:10 a.m. (21:40 GMT). Afghan forces backed by U.S. airstrikes have been fighting to dislodge Taliban insurgents who overran Kunduz on Monday. (Médecins Sans Frontières via AP)
Afghan security forces take a wounded civilian man to the hospital after Taliban fighter's attack, in Kunduz city, north of Kabul, Afghanistan, Saturday, Oct. 3, 2015. Three staff from Doctors Without Borders were killed and 30 were missing after an explosion near their hospital in the northern Afghan city of Kunduz that may have been caused by a U.S. airstrike. (AP Photo/Dehsabzi)
U.S. Forces-Afghanistan Resolute Support Mission Commander Gen. John Campbell testifies on Capitol Hill in Washington, Tuesday, Oct. 6, 2015, before the Senate Armed Services Committee hearing on the Situation in Afghanistan. (AP Photo/Carolyn Kaster)
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No evidence has surfaced publicly to support those conclusions about the Pakistani's connections or his demise. The former intelligence official was not authorized to comment publicly and spoke only on condition of anonymity.

The top U.S. officer in Afghanistan, Gen. John Campbell, has said the strike was a mistake, but he has not explained exactly how it happened or who granted final approval. He also told Congress he was ordering all personnel in Afghanistan to be retrained on the rules governing the circumstances under which strikes are acceptable.

The new details about the military's suspicions that the hospital was being misused complicate an already murky picture and add to the unanswered questions about one of the worst civilian casualty incidents of the Afghan war. They also raise the possibility of a breakdown in intelligence sharing and communication across the military chain of command.

Pentagon officials declined comment.

The international humanitarian agency that ran the facility, Doctors without Borders, has condemned the bombing as a war crime. The organization says the strike killed 12 hospital staff and 10 patients, and that death toll may rise. It insists that no gunmen, weapons or ammunition were in the building. The U.S. and Afghan governments have launched three separate investigations. President Barack Obama has apologized, but Doctors without Borders is calling for an international probe.

Doctors without Borders officials say the U.S. airplane made five separate strafing runs over an hour, directing heavy fire on the main hospital building, which contained the emergency room and intensive care unit. Surrounding buildings were not struck, they said.

Typically, pilots flying air support missions would have maps showing protected sites such as hospitals and mosques. If commanders concluded that enemies were operating from a protected site, they would follow procedures designed to minimize civilian casualties. That would generally mean surrounding a building with troops, not blowing it to bits from the air.

What the new details suggest "is that the hospital was intentionally targeted, killing at least 22 patients and MSF staff," said Meinie Nicolai, president of the operational directorate of Doctors without Borders, which is also known by its French initials MSF. "This would amount to a premeditated massacre. ... Reports like this underscore how critical it is for the Obama administration to immediately give consent to an independent and impartial investigation by the International Humanitarian Fact-Finding Commission to find out how and why U.S. forces attacked our hospital."

By one U.S. account from the scene, American and Afghan troops were under fire in the area.

Nicolai said in an email exchange that the group's staff "reported a calm night and that there were no armed combatants, nor active fighting in or from the compound prior to the airstrikes."

Doctors without Borders has acknowledged that it treated wounded Taliban fighters at the Kunduz hospital, but it insists no weapons were allowed in. Afghans who worked at the hospital have told the AP that no one was firing from within.

The airstrike came as U.S. advisers were helping Afghan forces take Kunduz back from the Taliban, which had seized the city.

The U.S. military's cursory description of what transpired has changed over time.

Initially, the military portrayed the incident as an accident stemming from the fog of war. American forces in the vicinity were under attack, a U.S. military spokesperson in Afghanistan said in a statement, and called in an air strike "against individuals threatening the force. The strike may have resulted in collateral damage to a nearby medical facility."

Two days later, Campbell told reporters that "Afghan forces advised that they were taking fire from enemy positions and asked for air support from U.S. forces."

He added, "An airstrike was then called to eliminate the Taliban threat and several civilians were accidentally struck."

The following day, however, Campbell told the Senate Armed Services Committee, "To be clear, the decision ... was a U.S. decision made within the U.S. chain of command. A hospital was mistakenly struck. We would never intentionally target a protected medical facility."

Asked about the location of any U.S. troops on the ground, Campbell said, "We had a special operations unit that was in close vicinity that was talking to the aircraft that delivered those fires."

His remark did not make clear whether any American on the ground had a direct view of the hospital. Military officials declined to answer questions, citing the investigation.

According to the former special operations officer, the commander on the ground has told superiors he was in the worst firefight of his career while taking fire from the building, which he said he did not know was a hospital. He requested the gunship strike. In that scenario, it's not readily apparent why his unit couldn't have retreated. The hospital is within a compound surrounded by a high wall that could have offered cover from fire emanating from one building.

The intelligence analysts who were gathering information about suspected Taliban activity at the hospital were located in various bases around Afghanistan, and were exchanging information over classified military intelligence systems. Typically, a decision to order a strike in a populated area would require many layers of approval and intelligence analysis of the potential impacts and civilian casualties.

Click through to see more of U.S. troops in Afghanistan:

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U.S. military (troops) in Afghanistan
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US analysts knew Afghan site was hospital
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 13, 2015, US army soldiers walk as a NATO helicopter flies overhead at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 14, 2015, US army soldiers load ammunition into rifles during a military exercise inside coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
US soldiers part of NATO patrol during the final day of a month long anti-Taliban operation by the Afghan National Army (ANA) in various parts of eastern Nangarhar province, at an Afghan National Army base in Khogyani district on August 30, 2015. Afghan security forces launched a joint anti-militant operation in three districts, killing over 150 armed insurgents and wounding 112 others with 13 security personnel killed and three others were wounded in the past 30 days, Afghan National Army Commander Zaman Waziri said. AFP PHOTO / Noorullah Shirzada (Photo credit should read Noorullah Shirzada/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 14, 2015, Afghan National Army (ANA) soldiers are served lunch at a kitchen inside a base in the Khogyani districtin the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 14, 2015, US army soldiers fire during a military exercise inside coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier stands guard at an Afghan National Army (ANA) base in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, US army personnel keep watch at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, US army soldiers play basketball at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 14, 2015, a US army soldier and military dog keep watch as Afghan National Army (ANA) soldiers walk through coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier takes aim during a military exercise at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 13, 2015, US army and Afghan National Army (ANA) soldiers walk as a NATO helicopter flies overhead at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 13, 2015, US army soldiers play chess inside coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier poses for a photograph at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier looks on with binoculars at Coalition forces Forward Operating Base (FOB) Connelly in Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier stands guard at an Afghan National Army (ANA) base in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, a US army soldier plays on a smartphone as he lies on a bed at coalition force Forward Operating Base (FOB) Connelly in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
TO GO WITH AFGHANISTAN-US-ARMY-CONFLICT-FOCUS BY GUILLAUME DECAMME In this photograph taken on August 12, 2015, US army soldiers walk past an Afghan National Army (ANA) base in the Khogyani district in the eastern province of Nangarhar. From his watchtower in insurgency-wracked eastern Afghanistan, US army Specialist Josh Whitten doesn't have much to say about his Afghan colleagues. 'They don't come up here anymore, because they used to mess around with our stuff. 'Welcome to Forward Operating Base Connelly, where US troops are providing training and tactical advice to the 201st Afghan army corps as they take on the Taliban on the battlefield. AFP PHOTO / Wakil Kohsar (Photo credit should read WAKIL KOHSAR/AFP/Getty Images)
A member of the U.S. Air Force stands guard, inside a C-130 Hercules aircraft, that belongs to the Afghan National Army, in Kandahar Air Field, Afghanistan, Tuesday, Aug. 18, 2015. Since the departure from Afghanistan last year of most international combat troops, Afghan security forces have been fighting the insurgency alone. Figures show that casualty rates are extremely high, reflecting an emboldened Taliban testing the commitment and strength of the Afghan military. (AP Photo/Massoud Hossaini)
U.S. military officers pay respect during a change of command ceremony in FOB Oqab, Kabul, Afghanistan, Monday, July 27, 2015. (AP Photo/Massoud Hossaini)
U.S. military vehicles stage at the site of a suicide attack that targeted a convoy of American troops in Jalalabad, east of Kabul, Aghanistan, Friday, April 10, 2015. An Afghan official says the bomb killed and wounded several civilians. The Taliban have claimed responsibility for the attack. (AP Photo)
U.S. Defense Secretary Chuck Hagel speaks to American troops during a visit in FOB Gamberi, Afghanistan, Sunday, Dec. 7, 2014. Hagel visited the Forward Operating Base to meet with Afghanistan military officials and visit with American troops stationed there. (AP Photo/Mark Wilson, Pool)
US military forces listen to U.S. Secretary of Defense Chuck Hagel speaking at Tactical Base Gamberi in eastern Afghanistan, Sunday, Dec. 7, 2014. Hagel was winding up a two day visit, his last to Afghanistan as secretary of defense. (AP Photo/Mark Wilson, Pool)
FILE- In this file photo taken Sept. 23, 2009, a column of U.S. Army mine-resistant armored vehicles (MRAPs) and Afghan National Army vehicles pass through a village during a joint patrol in the Jalrez Valley in Afghanistan's Wardak Province. As the United States military packs up to leave Afghanistan, ending 13 years of war, it is looking to sell or dispose of billions of dollars in military hardware, including its sophisticated and highly specialized mine resistant vehicles, but finding a buyer is complicated in a region where relations between neighboring countries are mired in suspicion and outright hostility.(AP Photo/Maya Alleruzzo, file)
US soldiers and service members with the NATO- led International Security Assistance Force (ISAF) attend a religious ceremony on Christmas Eve at Bagram military base in Kabul, Afghanistan, Tuesday Dec. 24, 2013. The commander of NATO forces in eastern Afghanistan spent Christmas Eve visiting U.S. troops at bases across the mountainous region to bring them holiday greetings and gifts for a few lucky soldiers. (AP Photo/Rahmat Gul)
In this Monday, Dec. 9, 2013 photo provided by the U.S. Department of Defense, Joint Chiefs Chairman Gen. Martin E. Dempsey, center, arrives at Kandahar Regional Medical Hospital to visit medical staff and patients in Kandahar province, Afghanistan. America's top military officer said Tuesday the U.S. does not intend to renegotiate a security deal with Afghanistan and that a full withdrawal of its forces from the country at the end of 2014 could reverse gains made by Afghan troops in their war against the Taliban. (AP Photo/D. Myles Cullen, DOD)
In this March 22, 2013, photo, U.S. Marine Major Christopher Bourbeau, deputy commander at the 1st Brigade, 215th Corps Afghanistan National Army Advisor Team, at Camp Garmser, Helmand province, in southern Afghanistan, staging a pop quiz on how to tie tourniquets for the Afghan army troops he advises. The Afghan soldier tied the tourniquet in just over 30 seconds. U.S. commanders trying to hand off war-fighting responsibility by the end of 2014 are encouraged by the uneven yet steady progress of fledgling Afghan security forces. (AP Photo/Kim Dozier)
A Chinock window gunner guards, near U.S. Secretary of Defense Chuck Hagel, on a helicopter over Kabul, Afghanistan, Sunday, Dec. 8, 2013. Hagel spoke with troops and thanked them for being deployed for the holidays. (AP Photo/Mark Wilson, Pool)
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It would be significant if U.S. intelligence had concluded that Pakistani spies were continuing to play an active role helping the Taliban. The U.S. and Afghan governments have long accused Pakistan of aiding the Taliban, but U.S. rhetoric on the issue has cooled over the past year as American-Pakistani counterterrorism cooperation has improved.

Yet it's possible that a staffer at a hospital in Afghanistan was working for Pakistan's intelligence service. Two days before the strike, Afghan defense officials accused Pakistan's intelligence service of playing a key role in the Taliban's seizure of Kunduz.

Disputes within the U.S. government about airstrikes have played out before. In December 2013, the U.S. military's Joint Special Operations Command bombed a group of people it considered militants, but whom outside groups claimed were civilians attending a wedding. Even after the CIA assessed that some civilians were killed in the strike, Pentagon officials continued to insist that all those hit were combatants.

The incident added an argument for some members of Congress who were resisting Obama's proposal to shift the CIA's drone killing program to the military.

WATCH: Doctors Without Borders demands investigation:

Doctors Without Borders Demands Investigation

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