Officials said 628 people were on board the ferry when it sank late on Friday.
The ferry had been pounded by waves for 10 hours during a violent storm between Borneo and Java.
At least 212 people have been found alive. Most were plucked from life-rafts or clinging to debris, while some swam ashore.
"I didn't know what else to do with so many dead bodies"
- Ferry survivor
However, about 400 remain missing in rough seas, officials say.
Aircraft have been dropping food and water to those spotted adrift in lifeboats, but the weather remains too poor to reach all of them.
A survivor who had been rescued from a life raft said on Wednesday that bodies had been dumped from his boat as people died before help could arrive.
"I was very sad when I had to get rid of the bodies. But I didn't know what else to do with so many dead bodies," Leopold Kafares, 35, said.
He was speaking at a hospital in Surabaya, East Java, where he was being treated after being picked up at sea.
Kafares said when the ferry ran into trouble in rough seas, passengers scrambled for life buoys or space in life rafts.
He "struggled to get into the craft with four other people" but said the others died in the rough weather conditions and with no food or fresh water.
He said he helped pull other people into the raft later, but some of those died too.
Scores of bodies have been sighted afloat or washed up on beaches.