Twenty-three personnel were quickly rescued following a "mishap" involving the MV-22 Osprey tilt-rotor, the primary assault support aircraft for the Marines yesterday.
But three marines remain missing despite a search operation supported by aircraft and ships.
"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.
"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."
It was in the region as part of the Australian-US joint military exercise Talisman Sabre, which has just concluded in Queensland state.