Fishermen found four people alive in a fish trap and took them to hospital in the town of Siwa on Sulawesi island, the head of the local rescue team, Roki Azikin told Reuters.
A transport ministry spokesman said another 21 people were later found at sea.
"(The boat) may be upside down now," Azikin said.
"Other passengers are still out in the sea wearing life jackets and we're evacuating," he added.
The ferry left the southeastern side of Sulawesi on Saturday morning and was heading across the Gulf of Bone for South Sulawesi, transport ministry said.
It was left adrift in rough seas off the coast of south Sulawesi on Saturday night after high winds prevented rescuers from reaching it.
It is unclear how many passengers and crew were onboard.
News website Detik.com on Saturday said 108 people were on the ship, while Kompas.com said it was carrying 122 people.
Three ships have been deployed to find the missing ferry, which police said was still afloat with a broken engine, but out of radio contact.