Twenty-three personnel were quickly saved following Saturday's incident involving a MV-22 Osprey tilt-rotor, the main assault support aircraft for the Marines.
But three marines remain missing despite an air and sea search.
"Operations have now shifted to recovery efforts. The next-of-kin for the three missing Marines have been notified," US Marines based in Japan said in a statement.
US military aircraft in 'mishap' off Australia
"As the sea state permits, recovery efforts will be conducted to further search, assess and survey the area, in coordination and with assistance from the Australian Defence Force."
Defence Minister Marise Payne said Sunday the Royal Australian Navy was deploying a survey ship, HMAS Melville, as well as a navy dive team to the area to help the recovery operation.
"Our thoughts are with all those affected by this tragic event and the Australian government stands ready to support the US further in any way we can," she added.
The Marines said the recovery and salvage operations could take several months to complete, while the cause of the crash was being investigated.
The MV-22, which is half-helicopter half-turboprop, has two engines positioned on fixed wingtips that allow it to land and take off vertically. It can travel much faster than a helicopter.
It was in the region as part of the Australian-US joint military exercise Talisman Sabre, which has just ended in Queensland state.
There have been a series of deadly incidents, mostly in the United States, involving the aircraft.
In April 2000 19 Marines were killed in an MV-22 crash in the US.
Locals on the Japanese island of Okinawa have protested against the deployment of the MV-22 to a US airbase in the middle of a crowded city.
In December a "controlled landing" of the controversial hybrid aircraft just off the coast during a training flight sparked local anger. The aircraft was in pieces after the incident but no one was killed.
Okinawa campaigners who want the base moved off the island say they cannot tolerate the possibility of accidents, as well as noise and crimes committed by US service members.
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