At least eight people, including a child, believed to be asylum seekers, were feared dead when their boat sank off Java while on its way to Australia.
While search is on to look for 15 missing people, a total of 57 people were rescued yesterday before the search was suspended due to poor weather.
Immigration minister Chris Bowen said it was "very clear" the nine-metre boat was heading to Australia.
According to an ABC report, at least eight people including a child were feared dead when their boat sank.
Australian authorities, meanwhile, confirmed another boat carrying 92 asylum seekers arriving at Christmas Island.
The deputy police commissioner for the area, Agus Santoso, was quoted as saying that bad weather and overcrowding may have contributed to the accident.
There were reports the local fishermen's association had been warning for days that conditions were too rough to go out in.
Bowen said the rescue operation was now likely to turn into a recovery operation for bodies.
"I think we can tragically assume that many, if not most of those people who are missing, will be very very difficult to recover alive," he said on Wednesday morning.
"The Indonesian authorities to my knowledge have not requested any assistance," he added.
"They are perfectly capable of handling a situation such as this, (and) of course we talk to them, because it's very clear this boat was heading to Australia.
Greens Senator Sarah Hanson-Young said the news of the deaths was "awful" and said the situation showed how desperate asylum seekers are.
"What this clearly shows is that we need to be offering safer pathways for people to reach protection and to ensure that they can seek asylum in a safe way," she said.
The Federal Government also confirmed another boat carrying 92 asylum seekers as having arrived at Christmas Island.
The President of the Christmas Island Shire, Gordon Thomson, said the boat arrived this morning and is in Flying Fish Cove with people still onboard.