One of those found alive was the captain of the ship, which had 118 on board when it ran into trouble and went down on Saturday in the Gulf of Bone off Sulawesi island.
"His physical condition is weak," Alamsyah, chief of the Disaster Mitigation Agency in the island's Wajo regency told Reuters. "They are setting up tight security around him, and he will be interviewed later for investigation purposes."
Forty-one people have now been found alive by rescuers in helicopters, fishing vessels and rubber dinghies, and three people have been declared dead.
"We will continue searching until the seventh day," Alamsyah said. "Considering that they have been out there for three times 24 hours, I am a little bit pessimistic, but we have found two more people alive today, so I am praying for these 74 people."
One survivor, a woman who gave her name only as Bertha, told the TvOne news channel that passengers had heard a crashing sound, then the ferry jolted and water gushed in as it listed.
She and her family members were tossed off the ship and into the sea where they were separated by towering waves.
"The wave was very big, like a mountain approaching, as big as a house," said the woman, whose grandson survived with her but three other members of her family were still missing.