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Jusman Syafi'i Djamal told Reuters that 150 people had been taken off the ferry, but added he did not know if they were dead or alive.
"There's a tropical cyclone now which caused tides of five to six metres," Djamal said by telephone.
He said the ferry had 250 passengers and cargo on board.
A transport agency spokesman earlier said 18 people were known to have survived, but did not give details.
The ferry left Pare-pare on the island of Sulawesi on Saturday and was heading for Samarinda, in East Kalimantan, but got into difficulties and sank at around 4 a.m. on Sunday morning, Taufik Bulu, head of maritime safety at Pare-pare port administration, told Reuters.
He said the ferry was carrying 250 passengers and 17 crew.
Indonesia relies heavily on ferry services to connect the main islands in the archipelago, the world's largest.
But accidents are common, largely because of years of under-investment in the country's infrastructure and a tendency to overload ferries.
Officials said a rescue was under way.
"Our people there are trying to save people now," said Bambang Ervan, spokesman for the Transport Ministry.