Search and rescue agency chief Bambang Soelistyo told AFP 13 corpses were found yesterday in the southern gulf of Sulawesi island, where the ill-fated ferry sent a distress signal before losing contact at the weekend.
"To date, we've evacuated 60 people," Soelistyo said.
"Forty have been found alive, and 20 dead."
The boat was believed to be carrying 116 people when it ran into trouble, Soelistyo said, citing passenger figures provided by the ferry operator.
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One of the last found alive was the ferry's captain, who like other survivors described massive waves smashing into the boat before the engine died and the order was made to abandon ship.
Footage shot by a passenger and aired on Indonesian broadcaster TVOne showed the ferry listing and partially submerged, with large waves buffeting the stern.
Many passengers could be seen floating in the water wearing life jackets.
"It depends on the result of the day to day operation," he said.
The Indonesian archipelago of more than 17,000 islands is heavily dependent on ferry services but fatal accidents are common.