Thirty-seven passengers were pulled alive from rough seas by rescuers in helicopters, fishing vessels and rubber dinghies after the boat ran into trouble on Saturday (local time).
Three people have been found dead in the Gulf of Bone off South Sulawesi.
The boat was carrying 118 people.
Roki Asikin, head of the local rescue team, told Metro TV the search for survivors would resume with daylight on Monday.
Alamsyah, chief of the Disaster Mitigation Agency in the island’s Wajo regency, said: “We’ve tried our best with all the equipment we have, with the help of the search and rescue team’s helicopters and its Pacitan ship. We are grateful for fishermen’s help”.
“But we are worried that more than 24 hours have passed. We are waiting for miracles, God’s miracles. We hope that all of them can survive.”
He said waves of up to three metres in height and strong winds had hampered efforts to find survivors during the day.
Many of those rescued were found with life jackets floating in the sea after they had abandoned the stricken ferry, and four people were found alive in a fish trap.
One passenger rescued by fishermen, who gave his name as Mussakar, told the TV One channel: “When the ship listed and was about to sink, everyone jumped. There was a lifeboat … but then it capsized and sank.”