The Marine Corps said earlier they had shifted from a search-and-rescue effort to a recovery operation, which could last several months, and had notified the next-of-kin of the three missing Marines.
"The transition comes after teams led continuous sustained search efforts supported by aircraft and ships," the III Marine Expeditionary Force, based in Okinawa, Japan, said.
"As the sea state permits, recovery efforts will be conducted to further search, assess and survey the area ...," they said in a statement.
The U.S. Marines have described the incident involving the MV-22 Osprey tilt-rotor aircraft as a "mishap" and said it was under investigation.
Ospreys have been involved in incidents resulting in deaths or injuries in recent years.
Australian Defence Minister Marise Payne said the Australian government would assist the U.S.-led recovery effort after what she described as an "extensive search-and-rescue operation" was called off.
"Our thoughts are with all those affected by this tragic event and the Australian Government stands ready to support the U.S. further in any way we can," she said in a statement.
Payne said a Royal Australian Navy survey ship was en route to the search area. A navy diving team would be sent soon and army aviation assets were "at short notice readiness to support any further requirements", she said.
Apart from the three missing Marines, 23 other personnel aboard the aircraft had been rescued. Australian emergency officials said one person had been taken to hospital in Rockhampton in northeastern Queensland state but gave no other details.
"All other personnel are accounted for and safe," the III Marine Expeditionary Force said on Twitter.
The incident happened off the coast of Shoalwater Bay in Queensland at about 4 p.m. local time on Saturday (0600 GMT), the Marine Corps said. They called off the search at about 3 a.m. on Sunday (1700 GMT Saturday).
Australia's Bureau of Meteorology described wind, swell and atmospheric conditions at the time of the incident as "benign".
"There was a light northeasterly wind with high cloud ... but that would have had no impact whatsoever on conditions at the surface," meteorologist Michael Paech said.
The aircraft that crashed had taken off from the USS Bonhomme Richard (LHD 6) amphibious assault ship and was on regular operations when it hit the water, according to the Marines Corps.
U.S. President Donald Trump, who was on his first full day of vacation at the Trump National Golf Club in Bedminster, New Jersey, was briefed on the crash by his chief of staff, retired Marine Corps General John Kelly, a White House official said.
The Bonhomme Richard Expeditionary Strike Group was in Australia to participate in joint training manoeuvres involving more than 33,000 U.S. and Australian military personnel, which ended two weeks ago.
The exercises in the Coral Sea included the participation of MV-22 Ospreys practising the deployment of U.S. Marine reconnaissance teams.
The Osprey, built by Boeing Co and Textron Inc's Bell Helicopter unit, is designed to take off like a helicopter and rotate its propellers to fly like a plane.
Its development was nearly cancelled after the deaths of 23 Marines during flight testing in 2000, but its speed and range have made it very popular in recent years.
In December, the U.S. military grounded its Osprey fleet in Japan after one of the aircraft ditched into the sea, injuring its crew of five, when a hose connected to the aircraft broke during a refuelling exercise.
(Reporting by Joseph Hinchliffe; Additional reporting by Valerie Volcovici in WASHINGTON; Editing by Mary Milliken and Paul Tait)
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)