Rescuers have pulled out at least 23 survivors and two bodies from a passenger boat that sank in central Indonesia after being buffeted by high waves.

Bad weather on Sunday made it difficult to reach scores of others still missing, authorities said.

The fibreglass boat was on its way to Siwa from Kolaka, towns on Sulawesi island, with 110 passengers and 12 crew when it was overwhelmed by waves reaching more than three metres during stormy weather on Saturday afternoon, said Roki Asikin, head of the search and rescue agency in Makassar, the provincial capital of South Sulawesi.

Six rescue boats and ships were sent from Kendari and Makassar after they received a distress call from the crew who reported that the vessel was starting to take on water about 21 kilometres southeast of Siwa port in Wajo district, Asikin said.

The passengers included 14 children, he said.

Earlier Sunday, fishermen found four people, including a woman and a child wearing life jackets. They told authorities their boat sank hours after being hit by high waves.

Transportation Ministry spokesman Julius Barata said that 21 others were found later by another boat of the same company as the sunken ferry.

"Latest report we received said a total of 25 people — 23 survivors and two deaths — have been discovered, and are now being evacuated to Siwa," Barata said.

Television footage showed dozens of family members anxiously waiting for their loved ones at the Siwa port.

Indonesian boat accidents have killed hundreds of people in recent years. Boats are often overcrowded and safety regulations are poorly enforced. The vast country spans more than 17,000 islands with a population of 250 million, and boats are a popular and relatively cheap form of transportation.