At least two people died after an overloaded boat believed to be making its way to Australia with hundreds of asylum seekers from the Middle East has sunk in heavy seas off the main island of Java over the weekend, ABC reported.

Local news said the boat had a capacity to carry 100 passengers but it was overloaded, and latest reports from Indonesia indicate 217 people are still missing as of Monday.

Sahrul Arifin from the East Java Disaster Mitigation Centre told ABC strong waves wrecked the wooden boat when it was cruising on the usual path taken by asylum seekers on their way to Australia's Christmas Island.

Eight people died when a boat capsized in the same area in November.

"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.

Arifin said the passengers are believed to be illegal migrants from countries including Iran and Afghanistan.

Local fishermen have rescued at least 33 people, while two bodies have been recovered.

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

As this developed, Australian Home Affairs Minister Jason Clare slammed the critics of the Government's onshore asylum processing policies and says the death of asylum seekers is a terrible tragedy and rescue efforts should be prioritized.

"This is a terrible tragedy. People have died, there are people still missing," he said on Sky TV Sunday.

"Our focus today is on the search and rescue efforts and our thoughts today are with the people who died and with the families of those still lost at sea," Clare added.