The body of one person was recovered and 71 people were rescued after the vessel sank on Tuesday evening while travelling between Kupang, the capital of East Nusa Tenggara province, and the island of Rote, the official from the procince's Search and Rescue Agency, who identified himself as Eri, told AFP.
"The boat's manifest shows that it was carrying 82 passengers and a crew of 20," he said.
Eri said that the boat had hit rough seas while heading for Rote and tried to turn back to Kupang, but that its engine had died. High waves then capsized it.
Three navy boats and a ship from the state-run ferry company were combing the area looking for survivors, Eri added.
Indonesia, the world's largest archipelago nation, relies heavily on marine transportation, but weak enforcement of safety standards has led to frequent accidents.