The pair, aged in their 20s, are recovering in the Thursday Island Hospital, off the tip of the Cape York Peninsula, the Seven Network reported.
The men, dehydrated and exhausted, were spotted on Saturday by a routine border patrol and were soon plucked from the ocean by an Emergency Management Queensland helicopter flown by pilot Terry Gadenne.
"When we winched down the rescue crewman into the water, the guy in the esky leapt out," Mr Gadenne told Seven.
"He was desperately keen to get on and pulled him (the rescuer) down into the water, so he was pretty keen to get away from the ocean.
"When they got up (into the helicopter) they skolled two litres of water each within seconds." The men said 18 other people were on board the ship but were thrown into the water.
They were lucky to survive, Australian Maritime Safety Authority spokeswoman Tracey Jiggins said.
"Given that they have been in the water 25 days, our Rescue Coordination Centre Australia has made an assessment that they would not be able to survive for that period of time without any form of a flotation device," she told Seven.
Immigration officials have been sent to Thursday Island to investigate whether the boat was being used for fishing or a people-smuggling operation, Seven said.
A spokeswoman for the Thursday Island Hospital told AAP she could not discuss the medical condition of the men.
