Nine Indonesian fisherman are believed to have drowned after their boat capsized off Western Australia's far northern coast.
Rescue crews were dispatched from Broome and Cairns in the early hours of Monday morning after reports of an incident near Ashmore Reef.
In a statement released late on Monday, the Australian Maritime Safety Authority said there were 12 people aboard the vessel, which was first seen at about 7pm on Sunday evening 180 kilometres west of Ashmore Reef.
Three fishermen were rescued, but the remaining nine remain unaccounted for.
"AMSA diverted the Singapore-flagged bulk carrier PSU Sixth, which rescued three survivors from the fishing vessel," a spokesperson said.
"The helicopter crew refuelled en route at a nearby oil rig before conducting a winch recovery of one survivor, who was critically ill, and recovering them to Broome hospital."
The man, aged in his 50s, was flown to Perth by the Royal Flying Doctor Service on Monday afternoon and remains in a critical condition.
He is expected to be transferred to Royal Perth Hospital.
"The two remaining survivors were transferred to an Australian Government vessel and are expected to arrive in Darwin tomorrow," the AMSA spokesperson said.
Reports wave struck ship
Indonesian media are reporting the wooden vessel left local waters on Thursday last week and ran into difficulty when it was struck by a large wave.
Weather in the area has been particularly rough due to the presence of Tropical Cyclone Charlotte, which formed on Monday, but has tracked through the area as a tropical low in recent days.
The report indicates the survivors are being supported by the Indonesian Consulate in Darwin and arrangements are being made to return them home.
Ashmore Reef is located in the Indian Ocean, about 630 kilometres north of Broome.
While authorities are yet to reveal full details of the incident, the area of Australian water between Ashmore and the Kimberley coast – and Australia's northern waters more broadly – have been heavily targeted by illegal fishing boats in recent months.
Australian authorities began escalating patrols of the area in response, intercepting 231 boats between July and December last year.
Twenty-nine vessels were seized and destroyed.
While the onset of the monsoon season was expected to slow fishing activity, local skippers told the ABC in December they expected the illegal activity to continue.
AMSA has extended its thanks to all involved in the rescue effort.
