HOPE is fast fading for as many as 100 people still missing after their boat capsized en route to Australia.

Indonesian and Australian authorities have rescued 109 people, including a 13-year-old boy, but have also pulled three bodies from the water.

Between 90 and 100 people are unaccounted for.

Home Affairs Minister Jason Clare says aircraft over the search and rescue area had spotted more bodies but no more survivors.

"We need to brace ourselves for more bad news," Mr Clare said on Friday.

The boat, crowded with asylum seekers, capsized about halfway between the Indonesian island of Java and Christmas Island on Thursday afternoon.

Most of the survivors were taken to Christmas Island on Friday.

Three men were receiving medical treatment at the island's hospital.

The search, led by HMAS Larrakia and HMAS Wollongong and assisted by a number of merchant vessels and several aircraft, was continuing into Friday night.

Mr Clare revealed that the boat's crew first made a distress call to Australian authorities on Tuesday night and another early on Wednesday.

Australian officials told them to turn around and head back to Indonesia, before telling Indonesian authorities of the boat's location.

A Customs and Border Protection surveillance plane spotted the boat on Wednesday afternoon but reported no visual signs of distress.

Mr Clare dismissed suggestions that Australian authorities could have saved lives by acting sooner.

"I'm not going to second-guess today the action they have taken other than to say it looks like they took proactive steps," he said.

Nonetheless, a full investigation into the incident would be undertaken, he said.

The Australian Maritime Safety Authority emphasised that the vessel was in Indonesia's search and rescue zone "at all times".

Asylum-seeker policy has been a hot political issue, with the government and opposition both blaming the other for an increase in boats since talks aimed at finding a bipartisan solution collapsed in January.

The government needs opposition or Greens support for a bill to underpin its Malaysian people-swap deal, which it believes would stop the boats.

Opposition Leader Tony Abbott said on Friday it was not the time to reignite the political debate.

"There'll be time enough in the days and weeks ahead to talk about what policy lessons might be drawn from it," Mr Abbott told reporters.

But senior Liberal backbencher Mal Washer said both parties were responsible for the political impasse that had led to the disaster.

"Somewhere in the cloud and smoke of politics of hung parliaments we got screwed up and we couldn't get the decency above the politics," Dr Washer told Sky News.

Dr Washer, the member for Moore in Western Australia, hinted he would consider crossing the floor to help get the government's bill through the House of Representatives.

But the bill would still stall in the Senate without wider support from the opposition or the Greens.

Independent MP Tony Windsor called for compromise.

"Surely the real issue is about saving people's lives and the best way of doing this is to discourage people from getting on a boat in the first place," Mr Windsor said.

The United Nations High Commissioner for Refugees (UNHCR) said the disaster underlined the dangers of people-smuggling boat journeys.

"The UNHCR calls on Australia and countries in the region to redouble their efforts to provide safer and more secure options for people to find protection other than through these dangerous and exploitative boat journeys," it said in a statement.

The Refugee Action Coalition's Ian Rintoul said more timely action by Australian authorities might have averted the disaster.

Originally published as 100 could be lost in asylum boat capsize