The search for survivors was abandoned late on Sunday, two days after the submerged vessel was first spotted in the sea.
At least 55 people were thought to have been on the boat, Australian authorities said.
Ships and aircraft had spotted a total of 13 bodies, as well as debris.
The boat was seen northwest of Christmas Island - the closest piece of Australian territory to Indonesia - on Wednesday, when it did not appear to be in distress.
A navy vessel subsequently went to intercept it, but could not find it. An aircraft spotted its submerged hull on Friday.
Officials said about 55 people had appeared to be on the boat. Their nationality was not known, but most of the asylum-seekers who make their way by boat to Australia via Indonesia come from Sri Lanka, Iraq and Afghanistan.
Figures from Australia's Department of Immigration; passenger numbers exclude crew
Both ships and aircraft searched for survivors over the weekend, but the Australian Maritime Safety Authority (AMSA) called off the search late on Sunday, citing medical advice that no-one could have survived any longer in the water.
Officials on Monday said they will not conduct a new search to retrieve bodies. "Our priority in those operations remains the protection of life, responding to other vessels which may require assistance, and preventing any further loss of life," a Border Protection Command statement said.
In recent months the number of people attempting to make their way to Australia by boat has risen significantly.
Last year, the government re-established offshore processing camps for asylum seekers in Papua New Guinea and Nauru in a bid to deter people from making the dangerous journey across the sea in overcrowded and poorly-maintained vessels.
But the offshore processing policy - and the conditions in the camps - have been heavily criticised by rights groups and UN agencies, and boat numbers have also continued to rise.
"This is another terrible tragedy, another terrible reminder how dangerous these journeys are," Home Affairs Minister Jason Clare said on Sunday.
Australian authorities have called off rescue efforts for a boat carrying asylum seekers that sank north of Christmas Island.