Defence chief Angus Houston said the unidentified boat capsized and then sank after the LNG Pioneer ship and Taiwanese fishing craft responded to pleas for help in a remote area off Australia's Cocos Islands in the Indian Ocean.

It was not confirmed whether the boat was one of dozens of people-smuggling vessels that have headed to Australia this year carrying more than 1,700 asylum-seekers, many of them from Sri Lanka and Afghanistan.

"I understand when the first ship got there, this vessel was still intact," Houston said.

"Somehow or other during the process of interaction between the ship and trawler and also the stricken vessel, there's been a capsize and people ended up in the water."

Some 17 people were rescued by scrambling aboard life-rafts thrown out by the LNG Pioneer, which was sailing to Western Australia when it diverted course to help the stricken boat.

A maritime safety official said there were "grave concerns" for the missing, while Prime Minister Kevin Rudd warned that finding more survivors would be difficult.

"Our assets have been deployed, we have co-ordinated with other vessels in the area. This is a very difficult search environment," Rudd told reporters.

A surveillance plane was headed to the area but a rescue ship was about a day's sail from the site off the tiny Cocos Islands, some 2,000 kilometres (1,250 miles) off the Australian coast.

"We obviously have grave concerns about the safety of those who are still in the water, given they've been in there for some time now," a spokeswoman for the Australian Maritime Safety Authority told AFP.

"The weather conditions aren't great, not too conducive to a search and rescue."

The boat started taking on water late on Sunday and issued a distress call, prompting a plea for help by Australian authorities, which was answered by the LNG tanker and Taiwanese fishing craft.

"The LNG Pioneer (merchant ship) is still conducting search and rescue now," the spokeswoman said. "It's throwing out its life-rafts in the hope of recovering more people from the water."

Home Minister Brendan O'Connor said authorities did not know whether the sunken vessel was carrying asylum-seekers, who are the subject of fierce domestic debate as the government struggles to deal with the influx.

"The purpose of the voyage has yet to be determined. At this stage efforts are being made to rescue those at sea," O'Connor told Sky News.

"We want to make sure that the safety and well-being of these passengers are the first and only matter that is of concern at this point. Once we've done that we can start to work through those other issues."

Australia has been forced to nearly double the capacity at its main refugee centre on Christmas Island in the Indian Ocean.

It is also involved in an ongoing stand-off over the fate of 78 rescued Sri Lankans, who are refusing to leave an Australian ship moored in Indonesia.

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