The vessel caught fire yesterday in the waters off the archipelago's main Java island, prompting the captain to order people to abandon the boat, the national disaster management agency said.
The agency said the fire might have caused by a short circuit in one of the trucks carried on board.
Rescuers have evacuated 141 people and recovered five bodies in the incident, the local chief of the search and rescue agency, Mochammad Arifin, told AFP.
Authorities were checking the manifest to determine whether anyone else was missing, Arifin said.
In January, 23 Indonesian tourists were killed when a massive fire erupted in a boat carrying hundreds of people to an island north of Jakarta to celebrate the New Year.