The boat capsized yesterday off the fishing town of Cidaun in western Java. Many of the people were still missing.
According to the Australian Associated Press, the vessel was believed to be carrying around 200 people from Iran, Iraq and Sri Lanka.
The sinking comes just days after Prime Minister Kevin Rudd changed Australia's refugee policy so that people who arrive by boat will no longer be allowed to settle there. The change has drawn sharp criticism from human rights groups.
Indonesian rescue officials said they did not know exactly how many were on board the vessel.
"So we're focusing on searching for any more that may be out there," Bandung search and rescue chief Rochmali said adding, "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."
Survivors gathered in two villages, Sukapura and Pantai Jayanti, and officials said they would be taken to hospital.
The country has experienced a sharp increase in the number of asylum-seekers arriving by boat in recent months. But critics have accused Australia of avoiding responsibility and passing on its problem to a developing nation.
Reacting to the incident, the news agency qouted Rudd as saying "All of our agencies are actively following this and ensuring that everything that can be done is being done."
He said the tragedy underlined the need for a tough asylum-seeker policy.
"We are seeing too many drownings, we are seeing too many sinkings, too many innocent people being lost at sea.
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