Rescuers were making last efforts Saturday to hunt for survivors from a refugee boat accident off Australia's Christmas Island as final hopes faded for some 90 people still missing.

Survivors arriving at Christmas Island 

The Australian Maritime Safety Authority (AMSA) said overnight searches of the sea north of remote Christmas Island had failed to find any more survivors, with the last living person plucked from the water late Thursday night.

One final effort was to be made Saturday, with medical advice suggesting there was still a chance someone could be alive, but the search was likely to be scaled back later in the day.

"We are continuing to focus on recovering survivors, however we will reassess the situation this afternoon and the focus may shift to recovering non-survivors," an AMSA spokeswoman told AFP.

"We will reconvene this afternoon and, based on what this morning's search uncovers, we will make a decision then."

Rescuers managed to save 109 people from the stricken people-smuggling ship which capsized with some 200 people on board in the Indian Ocean on Thursday afternoon, two days after first issuing a distress call.

Three people have been confirmed dead but there are fears for "around 90 people (who) remain unaccounted for" according to Customs.

The boat is believed to have originated in Sri Lanka and to have been carrying mostly Afghan asylum-seekers. The survivors include a 13-year-old boy.

Home Affairs Minister Jason Clare said the critical 36-hour search window had passed and conditions had steadily deteriorated, with the situation "looking grimmer by the hour".

"There may still be people alive, but we're passed that window," Clare told ABC Television.

"I've been on the phone to Border Protection Command. Their advice is that they've now instructed the men and women out in the search and rescue area to now identify people that have been perished and retrieve those bodies."

The capsize is the latest in a series of refugee boat disasters in the Indian Ocean in recent years, as rickety, overloaded vessels packed with desperate migrants struggle to reach Australia.

Most boats originate in Indonesia, though there has been a spike in attempts from Sri Lanka, with navy sources in Colombo telling AFP that people-smugglers had been encouraged by the failure of a so-called people swap with Malaysia.

That deal, under which Canberra would have taken 4,000 registered refugees in exchange for 800 asylum-seekers, was scotched by the High Court of Australia last year, forcing an easing in the government's mandatory detention policy.

Though they come in relatively small numbers by global standards asylum-seekers are a sensitive political issue in Australia, dominating 2010 elections due to a record number of boat arrivals.

The latest accident is the worst since 2001, when a crowded people-smuggling boat called the SIEV X sank, killing 353 of the more than 400 people on board.

Some 50 refugees were killed in a horror shipwreck on the cliffs of Christmas Island during a violent storm in December 2010, including 15 children -- one a baby just three months old.

A boat carrying around 250 mostly Afghan and Iranian asylum-seekers sank in Indonesian waters on its way to Christmas Island the following December, with only 47 surviving.