Immigration Minister Scott Morrison said Australian authorities had received a call about a vessel on Friday, which placed the boat about 25 nautical miles off Indonesia.
Despite an all ships broadcast issued by Australian authorities, a merchant ship failed to find the boat and it sank in rough seas, leaving at least 22 people dead and scores missing, including many children.
It had been carrying an estimated 120 asylum-seekers from Lebanon, Jordan and Yemen.
An Australian Border Protection Command aircraft also responded to the distress call but could not find the boat, Morrison said in the statement, reported by the Australian Associated Press.
"The Australian government expresses its deepest sympathies to those affected by this tragedy for their loss and will continue to provide any assistance required by the Indonesian government," Morrison said.
"Details of what has occurred are unclear at this time but it is understood Indonesian authorities are coordinating rescue operations.
"Australian government officials in Jakarta are seeking additional information from their Indonesian counterparts, including seeking to confirm where the vessel foundered. It is believed to have gone down in Indonesian territory."
Thousands of asylum-seekers have travelled by boat to Australia this year, many after a transit in Indonesia, and scores have died trying to make the journey in unseaworthy vessels over the years.
Australia is attempting to stop the boats via a policy that will see vessels turned around if safe to do so.
The issue will be on the agenda when Australia's new conservative Prime Minister Tony Abbott meets Indonesian President Susilo Bambang Yudhoyono in Jakarta on Monday.
Abbott refused to answer questions about the incident on Saturday. Friday's tragedy was the first deadly asylum boat accident since he became prime minister earlier this month.
Australian authorities have picked up at least one other group of asylum-seekers and returned them to Indonesia.
The boat, carrying 40 men and four children, made a distress call Thursday, and because Indonesian authorities were unable to reach the vessel quickly, Australians were tasked with the rescue.
The asylum-seekers, who were from Pakistan, Iran and Myanmar, as well as two Indonesian crew, were then taken close to Indonesia and transferred to an Indonesian vessel.
The Australian Broadcasting Corporation said an Australian Customs ship had also rescued a second boatload of 31 asylum-seekers and returned them to Indonesia.
COMMENTS (4)
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To pakistan- ur own people r leaving ur land of pure..
Still not able to understand why Muslims run to the west for asylum instead of the rich countries in ummah.
@zaman ali:
While I am also sad for the loss of life, they chose to take the risk and resort to illegal means to land in another land. The past history and facts show that more than 99.5% of the so-called asylum seekers are economic "refugees" who are not hesitant to flout the laws of other countries.
so sad to read this all their dreams and aspiration to start a new life, in a new, free and prosperous land, have drowned in the deep ocean with them. it's a sad reality that 90% of vasylum seekers in the west are from muslim lands.