Five suspected asylum seekers are feared drowned after they decided to swim from their troubled vessel using tubes and lifejackets.
Australian authorities found no signs of life as they searched the sea near the Cocos Islands on Sunday, with Home Affairs Minister Brendan O'Connor describing the situation as "tragic".
Another 59 passengers had been rescued from the boat by a Russian ship a day earlier.
The federal government first became aware of the boatload of asylum seekers nine days ago, when authorities were told it had run out of food, water and fuel about 230km north of the Cocos Islands.
But after a nearby merchant ship provided additional supplies, Border Protection Command allowed the boat to continue on its way to Christmas Island.
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Russian ship rescues vessel
On Saturday, the boat was rescued by a Russian ship and Australian authorities were told five people were missing.
"The passengers on the disabled vessel told the Russian crew that five people had decided to swim," the border protection spokesman said.
"But we're going to wait until we've interviewed these people to confirm anything like that."
The surviving passengers have been taken to the Cocos Islands, an Australian territory 3700km west of Darwin.
"If reports about five missing passengers are correct, this is a tragic and unnecessary loss of life, and highlights that these types of voyages are extremely dangerous," Mr O'Connor said in a statement on Sunday evening.
"Unfortunately, loss of life at sea can occur when people are persuaded to embark on these poorly maintained vessels over such a great distance."
Border Protection Command told AAP authorities started searching for the boat on Friday April 30.
"We were notified that there was a potential vessel requiring assistance," he said.
"We established contact with the vessel and discovered they'd run out of food, water and fuel."
A nearby merchant ship was called in to help. It transferred supplies but there was no additional request for assistance by the suspected asylum seekers.
"They were happy being in the boat," the spokesman said.
Search and rescue
Last Wednesday, when the boat hadn't arrived, the Australian Maritime Safety Authority (AMSA) was contacted "to conduct another search and rescue".
The boat was spotted again on Thursday by Australia aircraft about 280km from the Cocos Islands.
Four merchant vessels were sent to help with the Russian ship MV Postojna rescuing the passengers on Saturday.
Mr O'Connor said surveillance aircraft continued searching the rescue area on Sunday.
"Objects that may have been associated with persons missing have been identified, including lifejackets and tyre tubes," he said.
"However, advice received is that the search has not uncovered any signs of life."
The search has now been called off because the chances of survival are "no longer a reasonable possibility".
A spokeswoman for Mr O'Connor said the merchant ship which provided supplies on April 30 told authorities the suspected asylum seekers were okay.
"They advised AMSA that the vessel appeared seaworthy and the passengers told the vessel they didn't require any more assistance."
The boat was the 52nd intercepted trying to reach Australia this year.
