Twenty-four surviving passengers were admitted to hospital but dozens are believed still missing, said local disaster agency head Amiruddin, who like many Indonesians goes by one name.
The packed traditional wooden boat -- known locally as a jolloro -- left Makassar, provincial capital of South Sulawesi, in the afternoon for a short journey to the tiny resort island of Barrang Lompo, some 15 kilometers (9 miles) northwest of the city's coast.
"The boat reportedly hit a large wave amid bad weather and capsized," Amiruddin said.
The passengers were thought to be Barrang Lompo natives who work in Makassar and were heading home to spend the Islamic holiday Eid al-Fitr with their families.
Makassar police chief Aris Bachtiar said the boat was overloaded. "We are still investigating," he said, adding that the captain had been detained.
Almost 32 million Indonesians are on the move this week in the annual Eid exodus, official figures showed Wednesday.
It was the latest deadly maritime accident in the vast Indonesian archipelago, which relies heavily on boats to ferry people around its 17,000 islands but has a patchy safety record.
On New Year's Day, nine people died after a passenger boat capsized when travelling from the city of Tarakan to Tanjung Selor on Borneo island.
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