Indonesia's rescue agency was alerted by Australian authorities on Tuesday evening.
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"We don't know exactly how many were on board, so we're focusing on searching for any more that may be out there," Bandung search and rescue chief Rochmali told AFP early Wednesday, adding the figure would likely be between 100 and 200.
"We don't know where these people are from.
We will just focus on ensuring they're well and making sure no one else is still at sea," he said.
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The boat sank in heavy seas off the fishing town of Cidaun in western Java, from where rescuers set out in their own boats and in vessels lent by the police and fishermen.
Survivors would be taken to hospital, Rochmali said, adding the body of one child, the only confirmed dead, had been recovered.
Reports in Australia said the asylum seekers were mostly from Sri Lanka and Iran.
"I am the only one back," said a man named Soheil of a group of 61 Iranians he was travelling with, as quoted by the Sydney Morning Herald new