The wooden boat was carrying around 30 people when it overturned yesterday afternoon after departing from Takalar Lama river to Tanah Keke island in the province of South Sulawesi.
Twenty-one people have been found alive but rescue teams are still searching for missing passengers.
"It's a traditional boat and it didn't report to the relevant authorities before it departed, so there's also no passenger manifest and we don't know exactly how many people were on board," said local disaster agency spokesman Hamsidar, who goes by one name.
The fishing boat departed from an unofficial location, said a transport ministry spokesman, thus it did not have a legal permit to make the trip.
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The Indonesian archipelago of more than 17,000 islands is heavily dependent on boat transport but safety standards are poor and accidents occur regularly.
In January a passenger boat ferrying around 200 people from the capital Jakarta to nearby Tidung island left more than 20 people dead after it caught fire.
In November, at least 54 people died when an overcrowded speedboat carrying three crew and 98 passengers struck a reef and sunk on its way from Malaysia to Batam in Indonesia.