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There was hope that dozens more would be rescued after several liferafts were spotted at sea with people in them.
Anggit Mulyo Satoto, an Indonesian search and rescue official, said that some of the rafts had as many as 20 people in them but could not yet been reached because of the bad weather.
"Food and gear had been dropped to help them survive until rescued,” he said.
The state news agency said earlier that the bodies of 66 people had been located, many near Rembang on the coast of central Java.
However, a Rembang police official said that while fishermen who found the 66 assumed they were all dead, some may be still alive but unconscious, and the death toll was uncertain.
Susilo Bambang Yudhoyono, the Indonesian President, said he had urged rescuers to continue searching for survivors.
“I’m constantly in contact with officials on the effort to save our brothers and sisters,” he told a prayer session at the presidential palace.
Survivors in Rembang told harrowing stories of the ship’s last moments and their struggles to put on lifejackets and get into lifeboats before the Senopati Nusantara sank at about midnight on Friday.
One said the ship had started to roll over after struggling in high seas and heavy rains.
“Suddenly the lights went off and it became dark. The ship’s crew tossed lifejackets . . . some could not get any but I got one,” said Waluyo.
“I tried to get into a rubber boat but many people also did the same thing, so the rubber boat was torn. Finally, I grabbed the edge of another rubber boat.”
Waluyo, 53, said he did not know the fate of his children, one a young adult and the other an infant, travelling with him.
Another survivor, Yanti, said that many elderly passengers could not get into the lifeboats.
“Many old people were just resigned to their fate when the ship began sinking. I thank God for allowing me to live longer,” she said.
The Japanese-made 2,178-tonne ship was heading from Kalimantan on Borneo to Semarang in central Java. It was the second ferry disaster in as many days after a vessel overturned on Thursday in rough seas off Sumatra.
Two people on that ferry died and 26 were still missing, a rescue official said.
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