The editorial came after an Associated Press investigation revealed that many people outside government whom Clinton met with while she was secretary of state donated money to the foundation.
"'Pay-to-play' charges by Donald Trump have not been proved," the editorial said, referring to the Republican presidential nominee's attacks on the Clinton Foundation. "But the emails and previous reporting suggest Mr. Trump has reason to say that while Mrs. Clinton was secretary, it was hard to tell where the foundation ended and the State Department began."
The editorial argued that Clinton shouldn't wait until after the election to bar donations from foreign and corporate entities.
SEE MORE: Inside the Clinton Foundation donor list
Clinton Foundation donor list
Clinton Foundation donor list
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"The Clinton Foundation has become a symbol of the Clintons' laudable ambitions, but also of their tangled alliances and operational opacity," the editorial said. "If Mrs. Clinton wins, it could prove a target for her political adversaries. Achieving true distance from the foundation is not only necessary to ensure its effectiveness, it is an ethical imperative for Mrs. Clinton."
The Trump campaign released a statement on the editorial Tuesday, saying it pointed to Clinton's "poor judgment."
"The fact that even the liberal New York Times thinks the Clinton Foundation presents an unacceptable conflict of interest is a devastating rebuke of Hillary Clinton's poor judgment and broken ethical compass," said Jason Miller, a senior communications adviser for the campaign.
He added: "At a minimum, Hillary Clinton should heed the growing calls for her corrupt foundation to cease accepting foreign and corporate contributions immediately. With each donation she becomes more and more compromised."