An operation will begin today to recover the bodies of asylum seekers who are presumed to have drowned when their boat sank off Christmas Island.

Last night the Australian Maritime and Safety Authority (AMSA) from an asylum boat which sank last week with at least 55 people on board.

So far 13 bodies have been spotted in the water near where the boat went down, 65 nautical miles north-west of the island, but none have been recovered.

This morning Customs and Border Protection told the ABC it was not its job to recover the bodies and suggested contacting AMSA or the Australian Federal Police.

A Customs spokeswoman has since retracted that statement and says efforts to recover the bodies will begin today.

Boat spotted on Wednesday; first bodies seen on Saturday

The boat was first spotted by a Royal Australian Air Force aircraft late on Wednesday afternoon.

Customs aircraft sighted an upturned hull on Friday, but it was not until Saturday afternoon that dead bodies were seen floating in the water.

The three-day search for survivors involved a large air and sea operation coordinated by AMSA and involving up to three vessels, including HMAS Warramunga, and five aircraft.

The search was called off last night after medical advice that no-one could have survived in the ocean for that long.

Home Affairs Minister Jason Clare says those on board are believed to have been mostly adult men, but there were also a small number of women and children.

"This is another terrible tragedy. Another terrible reminder how dangerous these journeys are," he said.

The minister would not be drawn on the question of who is to blame but has foreshadowed a full review of the incidents after the operation is complete.

"We want to stop people getting here on boats," he said.

"At the completion of this search, this will be [the] subject of a full review, as is standard practice."

Refugee advocate raises AMSA resourcing concerns

Refugee advocate Ian Rintoul wants an investigation into why a search was not mounted from the moment the RAAF aircraft spotted the stationary boat.

He says he is concerned a lack of resources is hindering ASMA's search and rescue missions.

"We've seen too many of these instances where there have been issues about the slowness or the unwillingness of AMSA you know to respond appropriately and if there's an issue of resource then that needs to be public," he told AM.

"If we need more resources, so AMSA can respond in these kind of circumstances, then those resources should be made available.

"Until the Government puts policies in place so that people are processed in Indonesia and can be resettled out of Indonesia, people are going to continue you know to get on boats.

"If its policies are pushing people onto boats, then the least it can do, if it's not willing to escort boats, ... is make sure that there are the resources available so we don't see the loss of life at sea."

Greens call for humanitarian approach to asylum policy

Greens Senator Sarah Hanson-Young says the tragedy shows Australia's asylum policies are not working.

"We have the harshest policy that this country has ever had on asylum seekers at the moment, and yet people are still coming," she told ABC News 24.

"We have to find and be more insistent on providing people a safer alternative.

"Until we start responding to it as a humanitarian issue, not one of punishment, not one of deterring people from seeking asylum, it's going to make it very difficult to offer an approach that is humanitarian and humane."