Indonesian police are investigating three soldiers who are accused of being involved with the sinking of the asylum seekers' boat that sank off the Javanese coast on Saturday.

The boat, which is believed to have been making its way to find asylum in Australia, sank in rough seas with about 250 people on board.

Officials say about 30 bodies have been recovered so far, with hopes dimming for survivors in the violent waters.

ABC News reported the director of the General Crimes Division of Indonesia's national police force, Brigadier General Aridono Sukmanto said a group of soldiers is being investigated over the tragedy.

The group allegedly helped the people smugglers to organise the final stages of the asylum seekers' journey.

ABC further gathered from Indonesian police that people smugglers, some of whom have reportedly been identified, earned over $1 million from the 250 passengers.

At least 47 survivors were rescued from the ill-fated boat, which had a capacity of only 100 passengers, comprising of Afghan and Iranian asylum-seekers.

"Rescuers have brought 30 bodies to the shore while 10 others are on a navy ship heading to shore," East Java search and rescue agency chief Sutrisno told AFP. "There are still many bodies scattered and floating on the waters; we cannot tell you how many exactly... We found them floating in the waters near Banyuwangi district, 200 miles (320km) away from where the boat capsized."

Thirty-four people were rescued by fishermen on Saturday and 13 others were found drifting in a dinghy on Monday.

Survivors said crew members and asylum-seekers had fought over about two dozen life vests on the doomed boat, The Australian reported.

Meanwhile, the Australian Government and the Opposition remain in a political stand-off over asylum seeker policy. The Government has released a series of letters calling for talks between Immigration Minister Chris Bowen and his Opposition counterpart Scott Morrison, reports ABC.