"We are operating under conditions that include the water temperature, the weather, the fact that we now there were life jackets on board, rafts and debris," Ms Meehan said.
"At the moment we are operating on the basis that they will be able to survive for two days."
It was likely the rescue would turn to a recovery operation in the early evening (AEST), she said.
One hundred and nine people have been rescued since the crowded vessel capsized on Thursday afternoon about halfway between the Indonesian island of Java and Christmas Island.
Another three bodies have been pulled from the sea.
Between 90 and 100 people remain unaccounted for.
Most of the survivors were taken to Christmas Island on Friday, with three men treated at the island's hospital.
Customs and Border Protection and AMSA confirmed on Saturday that the safety authority received calls from a vessel "indicating it was experiencing difficulties" at about 10pm (AEST) on Tuesday.
"Later that evening, the location of this vessel was determined to be within Indonesia's search and rescue zone and as such the information was forwarded to (Indonesia's national search and rescue organisation) BASARNAS," customs said in a statement.
"There was no indication of where the vessel was located."
At around 1.30am (AEST) on Wednesday AMSA received more calls from the vessel, which was then reported to be 38 nautical miles south of the Indonesian mainland.
"AMSA advised the vessel to return to Indonesia if it was experiencing difficulty.
"AMSA advised the Indonesian Search and Rescue agency, who took responsibility to coordinate a response."
- AAP
