Officials called off the search for the day at sunset, with eight of the 49 people on board rescued, while the remaining 24 were still unaccounted for.
Twelve children are believed to have been among the passengers, though the number has yet to be confirmed.
"The search was called off in the evening because the waves were very big and it was getting dark," said national disaster agency spokesman Sutopo Purwo Nugroho, adding the search would resume tomorrow morning.
The wooden motor boat broke down yesterday after leaving from the east of the main island of Java late Monday.
"The engine was damaged and the water pump broke, so the boat filled with water and sank," Nugroho said.
Officials on Tuesday told AFP that the captain managed to briefly call authorities at around noon after the boat broke down but lost contact around four hours later.
The passengers on board are all believed to be Indonesian.
The eight survivors were rescued by helicopter, while several boats were deployed by the search team and fishermen were put on alert.
Indonesia relies heavily on boats to connect its more than 17,000 islands, but has a poor maritime safety record.
Boats are often overcrowded and not equipped with enough life jackets and rescue boats.
In August, a tour boat carrying 25 people sank after leaving the island of Lombok near Bali heading toward Komodo Island, a popular tourist destination.
The passengers were mostly European tourists, and two Spanish men were never found after the boat hit a reef and sank in stormy weather, with no working radio or satellite phone to alert rescue officials.
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