SURVIVORS from an asylum-seeker boat that sank off Indonesia claim their desperate pleas to Australian authorities for help were ignored as their vessel foundered in heavy seas.

The death toll from the tragedy was on Saturday expected to surpass 50, with 30 or so people still missing.

Indonesian authorities say that at least 21 people, including seven children, drowned when the boat, which was believed to be carrying about 80 passengers, sank on Friday off the coast of Java.

A decision on whether to resume the search would be made on Sunday morning, Indonesian officials said late Saturday.

The Australian government issued a statement on Saturday evening expressing its sympathies and saying that it would provide assistance to Indonesian authorities.

Immigration and Border Protection minister Scott Morrison said Australian authorities received a call about the vessel on Friday morning that placed the stricken boat about 25 nautical miles of Indonesia.

Mr Morrison said Rescue Coordination Centre Australia maintained co-ordination of the search and notified the Indonesian rescue agency.

An all-ships broadcast was issued by Australian authorities, but a merchant ship and a border protection aircraft were both unable to find the vessel.

The dead, wrapped in yellow bodybags, some stacked on top of each other, could be seen on Saturday, exposed to the sun and heat in an open storage room of a clinic in the village of Agrabinta, near where they had washed ashore the previous day.

Many were children.

One of the survivors, Lebanese man Hussein Khodr, had reportedly lost his pregnant wife and eight children in the disaster.

But some of the survivors say that more lives could have been saved, claiming that as many as 10 calls to Australian authorities were either eventually ignored or treated as a low priority.

"We called them and we told them we're sinking, we need anybody to help us," 28-year-old Abdullah al Qisi said, according to The Australian newspaper.

"And they were telling us 'we're coming, we're coming' and they didn't come," he said.

Initial reports suggested the boat first got into trouble about 10 hours into its journey and efforts were made to return to Indonesia before it sank.

There were also claims on Saturday that the crew had abandoned ship shortly after setting off, and that the passengers had been left to fend for themselves for five days, drifting around with no engine, before calamity finally struck on Friday.

A spokesman for the Indonesian search and rescue agency, BASARNAS, said his office was not advised of an incident involving an asylum-seeker boat until 8am local time on Friday.

He said the Australian Maritime and Safety Authority had contacted BASARNAS about the boat.

However, a police official from the district of Cianjur near where the boat sank said authorities were only alerted to the incident after bodies were discovered floating in an estuary on Friday morning.

Strong waves had limited search and rescue efforts on Saturday, although three more people were found alive, taking the number of confirmed survivors to 28.

It's the first known fatal attempted asylum-seeker crossing under the coalition government, which promised that it would stop boats reaching Australia after it won this month's federal election.

The sinking comes after another group of 44 asylum seekers were rescued by an Australian navy vessel in the Sunda Strait on Thursday.

It also emerged on Saturday that a third group of 31 asylum seekers had been rescued by an Australian navy vessel, and were set to be returned to Indonesia - the second "hand-back" in as many days.

The latest tragedy in waters between Indonesia and Australia comes amid an increase in tensions between Canberra and Jakarta over the asylum-seeker issue, and days ahead of talks in Jakarta between Prime Minister Tony Abbott and Indonesian President Susilo Bambang Yudhoyono.

Mr Abbott and President Yudhoyno will meet on Monday, with asylum-seeker policy expected to be at the top of the agenda.