Australia on Monday called off the search for bodies from last week's horrific asylum-seeker shipwreck, as the Prime Minister said about 48 people had died and warned the exact toll may never be known.

Prime Minister Julia Gillard said the "best estimate" was that around 90 people were on the wooden fishing boat which shattered on rocks at remote Christmas Island last Wednesday in a storm, as helpless residents looked on.

Only 42 people were rescued before the search for survivors was called off late Friday.

"We may never know the precise number but the advice to me is that the best estimate at present is that there were around 90 people on the boat," Ms Gillard told reporters, quoting police figures.

"That does mean of course that we are still not able to account for around 18 people."

Thirty bodies were retrieved after the accident, including a number of babies and children, before the search was terminated Monday on "advice from experienced the police divers that no further bodies would be found," Customs told AFP.

It is the worst disaster involving an asylum-seeker boat bound for Australia since the sinking of the SIEV-X off Indonesia in 2001, when all 353 on board died.

Ms Gillard said it may never be known "absolutely, certainly, how many people were on the boat," with authorities relying on accounts of survivors to try and establish how many people are still missing and their identities.

She said the increased toll "is obviously very very grim news and I am sure that Australians are on Monday continuing to reflect on this tragedy."

Survivors say the vessel was packed with Iranians, Iraqis and Kurds when it foundered on a rocky outcrop at Christmas Island, the site of Australia's main immigration detention centre and some 2,600 kilometres from the mainland.

The grim task of identifying the victims was underway at the hospital morgue Monday.

The Police have interviewed three Indonesian crewmen rescued after the crash and expect to lay charges, though they have declined to comment on whether these will include manslaughter.

One survivor whose husband and young son are missing told the West Australian newspaper the crew cut the boat's engine as it approached the island's rugged coast, assuring passengers the navy would come to their rescue.

Turning people-smuggling boats back at sea was government policy under the conservative administration of John Howard, prompting incidents where the vessels were sabotaged to ensure passengers were taken onshore in Australia.

The Police say there was nothing to indicate the doomed boat had been sabotaged.

The centre-left labor party wound back the harshest aspects of Howard's refugee policy, but legal experts said killing engine power in Australian waters was likely still a "habit" of people smugglers to spark a rescue.

Almost 6,500 refugees mostly from Iraq, Afghanistan and Sri Lanka have arrived in Australia this year on boats from Indonesia, crowding centres to capacity and inflaming debate on Canberra's tough mandatory detention policy.

Prayer services have been held at Christmas Island's immigration detention centre -- Australia's largest refugee camp — with a number of inmates mourning relatives and friends lost in the wreck.

Another boat was intercepted late Sunday carrying 56 passengers the 132nd since January.

Ms Gillard said the government would push ahead with plans for a regional processing centre for refugees, which it hopes will be built in East Timor, in a bid to "smash" the people-smuggling trade.