The long wooden boat carrying 35 passengers went down in the waters off Sula islands after it was hit by towering waves in rough weather, National Disaster Management Agency spokesman Sutopo Purwo Nugroho said.
"Of the 35 passengers, nine survived, 14 died and 12 are still missing," he said, adding that a rescue team comprising of police and military officials were searching for the missing victims.
Provincial disaster official Hasan Ahmad said all the passengers were Indonesian.
"There's no foreigner on the boat. We are still trying to find other survivors," he added.
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Indonesia relies heavily on boats to connect its more than 17,000 islands, but has a poor maritime safety record.
Eighteen foreign tourists and five Indonesians survived after their boat hit a reef and sank in stormy weather last month as they were travelling from Lombok island to Komodo island, a popular tourist destination.
Two vessels sank in July in different parts of the archipelago as millions travelled for the Muslim Eid holiday, leaving at least 36 people dead.