The boat sank shortly after midnight about 2 nautical miles (3.7 kilometers) from shore on the outskirts of Kuala Lumpur while trying to leave Malaysia illegally for Indonesia, said Mohamad Hambali Yaakup.
He said survivors included 12 women and a child. The Indonesians were believed to be heading home ahead of the start of the holy Muslim month of Ramadan.
They were being questioned by police and immigration authorities, and Indonesian embassy officials were also on the scene.
A ship and several boats were searching for further survivors.
He said authorities are still investigating the reason why the boat sank.
Tens of thousands of Indonesians work illegally in plantations and other industries in Malaysia. They often risk dangerous journeys in poorly equipped boats to return home.
The area the boat sank is in the Strait of Malacca directly across from Indonesia.