The Australian Maritime Safety Authority also says three seriously injured people are being treated on board the naval vessel HMAS Maitland.
Six men were plucked from the sea early on Thursday by merchant vessel APL Bahrain.
Another 16 were spotted from the air in the afternoon and were later picked up by HMAS Maitland, and another 23 were recovered by merchant vessels in the area. The circumstances under which another ten people were found are not yet known.
An Indonesian search and rescue vessel, as well as a police patrol boat, were to meet with the APL Bahrain to transfer its survivors to the port of Merak in western Java.
They will be taken to Merak, Indonesia, for medical attention.
All were on a boat carrying up to 150 people on its way from Indonesia to Australia.
Two distress signals were received from the boat early on Wednesday morning off Java's western-most tip, but a search failed to find them.
AMSA said the search and rescue, being conducted in coordination with Indonesian search and rescue agency BASARNAS, would continue through the night.
HMAS Maitland and four merchant vessels are on the scene looking for survivors.
Home Affairs Minister Jason Clare said the initial call of distress from the boat said the boat was carrying women and children.
Mr Clare lashed out at the people smugglers this morning saying the smugglers were running a "closing down sale'' by tempting refugee hopefuls with the offer of a ride to Australia before offshore processing rules kick in - and warned their opportunistic grab for asylum seekers’ money could continue.
"They're telling people they're selling them a ticket to Australia,” he said. "What they're really doing is selling them a ticket to Nauru or a ticket to the bottom of the sea''.
Mr Clare said the passing of legislation for offshore processing had fueled the people smugglers to act quickly.
"I think the legislation (to set up offshore processing) only encourages people smugglers to try and get people onto boats as quickly as they can because they know setting up offshore processing in Nauru, in Manus Island...will shut down their business model,'' he said.
"More than 300 people have died in the last three months and it appears more people have died in the last 24 hours.''
Mr Clare said he expected people smugglers to keep trying to sell asylum seekers tickets to Australia, saying some asylum seekers had already paid half their ticket.
"My message to them, is don’t get on the boat,” he said.
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