Indonesian officials say a boat carrying hundreds of asylum seekers from the Middle East has sunk in heavy seas off the main island of Java.

The Australian Government says about 250 people were on board the wooden boat, which was believed to be heading for Australia, but some news reports put the figure at 380.

Last month, eight people died when a boat capsized in the same area.

Local fisherman have helped to rescue 33 people so far, while two bodies have been recovered.

Sahrul Arifin from the East Java Disaster Mitigation Centre says strong waves wrecked the wooden boat when it was about 90 kilometres out to sea.

"Our search and rescue team have begun sweeping the water around where the accident took place, but we are now sending body bags to that area," he said.

He says the passengers are believed to be asylum seekers from countries including Iran and Afghanistan.

A search and rescue spokesman says extremely bad weather and poor visibility is making their work difficult.

As a result, two Indonesian navy ships and hundreds of sailors have been called in to continue the search.

"It is somewhat difficult to go on with the search because extreme weather has caused reduced visibility," search and rescue team member Brian Gauthier told state-run news agency Antara.

Mr Gauthier says some of the rescued are receiving assistance in the town of Prigi in eastern Java, around 30 kilometres from where the boat sank, adding that the rescue team believed some passengers were still alive and were likely suffering "severe dehydration".

"They must be evacuated as soon as possible. They can't stay for long in the middle of the sea," he said.

The Australian Government has also offered assistance in the search for survivors.

Home Affairs Minister Jason Clare says the boat sank about 7:00am (local time) and Australia was informed this morning.

He says Australia is offering an Orion aircraft but he has grave fears about finding survivors given they have been in the water for over 24 hours.

"Obviously grave fears are held for those on board," he said.

Local TV showed images of more than a dozen shocked survivors huddled in a clinic in Trenggalek, a town on Java island's southern coast.

One survivor from Afghanistan, 24-year-old Esmat Adine, gave rescuers an estimate of how many passengers were on the boat.

"He did not know exactly how many passengers there were, but he said that four buses with around 60 or more adult passenger each had turned up to the port where they set off," a translator for Mr Adine said.

Mr Adine said the boat, believed to be a traditional fishing vessel with a capacity of about 100, had been heading towards Christmas island.

Policemen carry an injured man to a local health clinic for treatment in Trenggalek, East Java. ( Dimas Aro: Reuters )

Asylum policy

Many asylum seekers from the Middle East and Asia use Indonesia as a transit point en route to Australia.

Opposition immigration spokesman Scott Morrison said the Coalition was profoundly saddened by the tragedy.

"While these events did not take place in Australia's waters they are equally devastating and equally tragic," he said in a statement on Sunday.

The Coalition said it supported all Australian government efforts to support the Indonesian rescue and recovery operation.

"The report of this tragedy once again confirms our worst fears and the extremely dangerous nature of these journeys, especially at this time of year," Mr Morrison said.

The large number of people reported to have been on the vessel was especially concerning, he said.

"It confirms the trend we have seen this year of the people smugglers putting more and more people onto every boat."

Home Affairs Minister Jason Clare has responded angrily to the criticism about the Government's onshore processing policies and says today's focus must be on rescuing survivors.

"I'm not going to go into the politics of this. People have died," he said.

"Today is not the day for politics - there'll be plenty of time for that. There'll be plenty of time to talk about the politics of this issue in the days ahead."



ABC/wires

Editor's note: (January 9) the original article incorrectly reported that the passengers were illegal migrants.