Captain Eleanor LeBeau, 29, Corporal Spencer Collart, 21, and Major Tobin Lewis, 37, died while taking part in a military exercise on Sunday when their MV-22 Osprey aircraft plunged on remote Melville Island, 80km north of Darwin.
Captain LeBeau was the pilot, Corporal Collart was crew chief and Major Lewis was squadron executive officer.
All three had been awarded numerous service medals.
The Darwin Marine Rotational Force (MRF-D) said the remains of the three marines arrived in Darwin about 6.30pm on Tuesday.
"The cause of the incident remains under investigation," a statement from the force said.
"One marine remains in a critical condition and has been transferred to The Alfred Centre (in Melbourne).
"Two other marines remain in Royal Darwin Hospital in a stable condition."
Twenty were injured in the crash but most have been discharged.
A candlelight vigil attended by about 50 marines was held at sunset in Darwin on Monday.
Earlier, commanding officer of the MRF-D Colonel Brendan Sullivan thanked Australian agencies for their efforts.
"We are deeply saddened by the loss of three respected and beloved members of the MRF-D family," he said on Tuesday.
"At present, we remain focused on required support to the ongoing recovery and investigative efforts.
"We would like to express our sincere gratitude to the Australian Defence Force, Northern Territory Police, Northern Territory government, CareFlight Air and Mobile Services, NT Health, National Critical Care and Trauma Response Centre and Tiwi Island government, who have come together to assist us in this difficult time."
An emergency call came through from air traffic control at the time of the incident, with an American voice asking for help.
"We are just declaring an emergency, we have Dumptruck 11 flight single MV-22 in the vicinity of Melville Island," the voice said.
"Contact 33, search and rescue is requesting … if there is fire?" an Australian voice asked six minutes later.
"There is a significant fire in the vicinity of the crash site. Looks like it is not spreading, but there is a significant fire," responds the American voice.
Emergency services plan to be at the site for more than a week as they work through what led to the tragedy.
"This recovery and investigation will be prolonged, enduring and complex," NT police commissioner Michael Murphy said on Monday.
"We are planning to be at the crash site for at least 10 days."
The Department of Defence said the incident occurred during Exercise Predator's Run 2023 and no Australian members were involved.
The Marine Osprey aircraft has a tumultuous history, with a number of mechanical and operational issues since its introduction in the 1980s.
Since 2012, 19 people have died in six crashes involving the Osprey which is used by the US and Japan.
About 150 US marines are stationed in Darwin for the military drills alongside personnel from Australia, the Philippines, East Timor and Indonesia.
Exercises on the island have been cancelled but mainland exercises have resumed.
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