Rescuers plucked 55 survivors from the ocean on Thursday, more than a day after an asylum-seeker boat heading for Australia disappeared off the Indonesian coast with 150 people aboard.

After Indonesia abandoned its search, six people were rescued overnight by a cargo ship and 49 more were pulled from the water by an Australian navy crew after being located by spotter planes late Thursday.

"The vessels have recovered 55 survivors. Three have serious injuries but are in a stable condition," the Australian Maritime Safety Authority (AMSA) said, adding that the search was being scaled back.

"Vessels will remain on scene overnight, but have limited search capability until daylight Friday."

The head of Indonesia's rescue mission at Merak port in western Java said it appeared that one of the survivors had been bitten by a shark.

Indonesia's National Search and Rescue Agency (Basarnas) received an alert from AMSA early Wednesday that a boat was in distress between Java and Sumatra, 220 nautical miles from the Australian territory of Christmas Island.

Basarnas sent two police rescue boats and a helicopter but found nothing and returned to base, only for AMSA to task the cargo ship APL Bahrain, which responded to an earlier broadcast to shipping, to attend a broader search area.

The captain of the Bahrain said screams and whistles alerted his crew as it scoured the Sunda Strait in darkness.

"We were doing scheduled searching. At the last moment when I was thinking to abort, I heard some noises, and we spotted them in the water," Captain Manuel Nistorescu told the Sydney Morning Herald's website.

"I (sent) a crew to get them and it was not easy... It was dark."

He said the rescued men appeared to be in good condition, adding that they said the pump on their boat failed and the vessel began taking on water.

"They had an engine break and the water was coming, and the pump for pumping out the water was not working and the boat sinks. This is what I understand from them," he said.

Australian Home Affairs Minister Jason Clare said there were serious concerns for those still missing, who include women and children.

"We have grave fears for a lot more," he said. "Don't underestimate how hard it is to find people in the middle of the sea."

AMSA said the survivors were expected to be taken to Merak in Indonesia's Java for medical attention. An Indonesian rescue boat carrying doctors was steaming to the area where the boat sank along with a police ship.

Four merchant vessels were continuing the search alongside HMAS Maitland and two Australian P3 Orion aircraft.

Australia is facing a steady influx of asylum-seekers arriving by boat, many of whom use Indonesia as a transit hub, paying people-smugglers for passage on leaky wooden vessels after fleeing their home countries.

Canberra this month said 300 boat people had died en route to the country this year, with vessels being intercepted by the Australian navy on almost a daily basis.

Two weeks ago, Canberra announced its intention to transfer asylum-seekers to Nauru and Papua New Guinea in the Pacific as part of a tough new policy to deter them from making the dangerous sea voyage.

But more than 1,000 boatpeople have arrived since the policy was adopted.

"My message to them is, don't get on the boat," said Clare.

"What we've seen today is there is a real risk people will die... that people will end up at the bottom of the sea."