Investigators have the task of determining what caused the US military Boeing MV-22B Osprey tilt-rotor aircraft carrying 23 marines to crash on Melville Island, 80km north of Darwin, on Sunday morning.
"There were a total of 23 personnel on board," Marine Rotation Force - Darwin said in a statement on Sunday.
"Three have been confirmed deceased while five others were transported to Royal Darwin Hospital in serious condition."
The rescue operation was ongoing overnight and the cause of the incident is under investigation.
Royal Darwin Hospital declared a Code Brown in response, the country's highest level of alert, with NT Chief Minister Natasha Fyles committing all resources to transport the injured marines to hospital.
The site of the crash has been secured by defence force personnel and NT Police while the military training exercise the troops were involved in has been put on hold.
Chief Commissioner Michael Murphy said workers at an emergency operation centre set up to tackle fires in the territory had been redeployed to the crash site, with the national critical care and trauma response team triaging patients before they were transported.
He said the remote nature of the incident made the rescue operation challenging, with both helicopters and fixed-wing aircraft involved.
The Department of Defence said the incident occurred during Exercise Predator's Run 2023 and no Australian Defence Force members were involved.
Prime Minister Anthony Albanese, speaking in Karratha, said the Australian Defence Force was working with its US partners to offer any assistance needed.
"Our focus as a government and defence department is on incident response and support at this difficult time," he said.
"Obviously this is a regrettable incident."
In a joint statement on Sunday night, Mr Albanese and Defence Minister Richard Marles said Australian and US personnel "have stood shoulder to shoulder for more than a century".
"This incident is a reminder of the significance of the service undertaken by our personnel and those of our partner nations," the statement said.
Opposition defence spokesman Andrew Hastie said the accident was a reminder of Australia's bonds with the US, "forged through sacrifice, in peace and war".
"We have an ongoing mission in preparing for the strategic challenges ahead, including navigating the tough geography of the Indo-Pacific region," he said in a statement.
"We will continue to train hard together as we defend our sovereignty, values and common interests."
The US embassy on Monday issued a statement thanking members of the rescue operation.
"Australians and Americans have been the closest of friends for over 100 years and we're thankful for their continued friendship and support at this time," it said.
RSL Australia President Greg Melick said the three deaths and injuries were "a tragic illustration of the everyday risks faced by service personnel".
"This is a catastrophic event, and we express our sympathy to the friends, families, and colleagues of all those impacted." he said in a statement.
About 150 US Marines are stationed in Darwin and taking part in military drills alongside personnel from Australia, the Philippines, East Timor and Indonesia.
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