Search and rescue teams were continuing to scour the Sunda Strait tonight as hopes continued to fade for many of the 150 asylum seekers who had been aboard the wooden boat.
Six men were plucked from the sea early on Thursday by the merchant vessel, the APL Bahrain.
Another 16 were spotted from the air this afternoon and were later picked up by the Australian naval vessel, HMAS Maitland.
An Indonesian search and rescue vessel, as well as a police patrol boat, were due to meet with the APL Bahrain at about 4.30pm local time (1930 AEST) in an effort to unload the survivors and transfer them to the port of Merak in western Java.
Almost 300 asylum seekers have already died along the same route, in the Sunda Strait between Java and Christmas Island, since December.
The latest incident will see that toll rise even further.
As the search continued, questions were also being raised about the initial response to the unfolding tragedy.
The boat had been on its way to Christmas Island when its pump failed, prompting a distress call to the Australian Maritime and Safety Authority (AMSA) at about 1.30am local time (1630 AEST) on Wednesday.
However, a search coordinated by the Indonesian search and rescue agency, BASARNAS, initially failed to locate the sinking boat or any survivors.
That search was then abandoned.
It was not until early Thursday morning that the first survivors were found after AMSA provided the Indonesians with an updated likely position for the boat based on drift modelling.
The Bahrain, which had responded to an earlier broadcast to shipping, was then tasked to attend the broader search area.
It appears the arrival of the Bahrain and other merchant vessels, almost 24 hours after the boat sank, may have been too late for many of the asylum seekers.
Australia’s Home Affairs Minister Jason Clare on Thursday defended the search effort.
"Don’t underestimate how hard it is to find people in the middle of the sea," Mr Clare said.
"It’s very, very hard and authorities have been working this issue since the time they got the original information yesterday morning."
Mr Clare also warned that people smugglers were rushing to get people on boats before detention centres on Nauru and Papua New Guinea’s Manus Island are up and running.
"People smugglers are running a closing down sale," he said.
The comments come ahead of a visit by Mr Clare to Jakarta next week where the issue of search and rescue is set to be discussed.
Plans to boost maritime co-operation between Australia and Indonesia, aimed at stemming the flow of asylum seeker boats to Christmas Island, are also expected to feature on the agenda.
