A search continued Friday for scores of men still missing after a boat carrying about 200 suspected asylum seekers bound for Australia capsized in heavy seas south of Indonesia.

Indonesian and Australian navies as well as civilian ships and aircraft had joined the search for around 90 people still missing after the tragedy Thursday.

All aboard the vessel were male, Australia's Home Affairs Minister Jason Clare said Friday.

An Australian navy patrol boat and three cargo ships had rescued 110 survivors — including a 13-year-old boy — by late Thursday and were taking them 200 kilometres south to the Australian territory of Christmas Island, Clare said.

The bodies of another three were also recovered from the water, Australian Maritime Safety Authority spokeswoman Jo Meehan said.

Clare said while seas were rough, people could have survived if they had life-jackets or were clinging to debris as most survivors had done.

"There is the prospect that there are people out there still alive," he told reporters.

He said about 40 survivors had been found clinging to the upturned hull on Thursday afternoon, while others were discovered clinging to debris up to six kilometres from the scene.

Clare said the boat had initially called Australian rescue authorities early Wednesday to report being "in distress" 70 kilometres south of the main Indonesian island of Java.

Australian authorities advised the crew to return to Indonesia and reported their situation to their Indonesian counterparts, he said.

The boat capsized about halfway between Christmas Island and Indonesia.

Authorities have not confirmed where the men were from, but Australian Broadcasting Corp. reports they are thought to be from Sri Lanka.

Christmas Island, in the Indian Ocean, is closer to Indonesia than the Australian mainland. It is a popular target for a growing number of asylum seekers, many from Iran, Afghanistan and Sri Lanka, who attempt to reach Australia on overcrowded fishing boats from Indonesia — sometimes with deadly consequences.

Western Australian police were being sent to Christmas Island to attempt to identify bodies.

Gagah Prakoso, a spokesman for Indonesia's Search and Rescue Agency, said two Indonesian warships had been dispatched to the scene.

He said Indonesia has sent notice to all cargo ships passing near the area to help.

Prakoso said the boat was reportedly carrying 206 people.

Australia sent a defence aircraft equipped with life-rafts, an Australian Customs Service surveillance aircraft and two navy patrol boats.

Australian Prime Minister Julia Gillard, who is seeking ways to stem the flow of asylum seekers to Australia, discussed the apparent tragedy with Indonesian President Susilo Bambang Yudhoyono in Brazil where they are both attending a United Nations environment summit.

"At this stage, details are sketchy but what is apparent is there has been a large loss of life at sea," she said. "This is a very distressing and tragic incident."

In December 2010, an estimated 48 people died when an asylum seeker boat broke up against Christmas Island's rocky coast.

Last December, about 200 asylum seekers were feared drowned after their overcrowded ship sank off Indonesia's main island of Java.