Australian and Indonesia warships joined merchant and government vessels to search for about 90 people missing after their steel-hulled fishing boat overturned some 140 miles south of Java, The New York Times reported.
Australian Maritime Safety Authority officials said 110 survivors had been rescued and taken to Australia's Christmas Island, the destination of their ill-fated vessel. Three bodies had been pulled from the sea.
The asylum-seekers are believed to be from Sri Lanka but the Australian government had not confirmed their nationalities.
All of the vessel's passengers were believed to be men.
The incident is the latest boat disaster involving asylum-seekers trying to reach Australia.
In December 2011, about 200 asylum-seekers were believed to have drowned after their overcrowded vessel sank off Java. In December 2010, about 48 people died after their boat broke apart against the rocky coast of Christmas Island.