Rescuers are still looking for another 128 people who were on board the boat Wednesday when someone made a distress call to Australian authorities and reported engine trouble.
Many of those rescued Thursday spent more than a day in the water southwest of Java.
Australian Home Affairs Minister Jason Clare says there are "grave concerns" for those yet to be found.
Asylum seekers frequently attempt the dangerous trip from Indonesia to Australia's Christmas Island, often with the aid of smugglers.
Officials say nearly 1,000 people have died trying to reach Australia by boat since 2001.
Australia recently passed new laws to try and deter such trips by setting up offshore processing camps for asylum seekers.
Right groups criticize the plan, saying it is a major setback for Australian refugee policy.
