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.
"We will continue to ask the United States (to refrain from flying Ospreys) until we receive a solid explanation" about the accident, Onodera told reporters after an Osprey crashed off the coast of Queensland state Saturday, leaving three U.S. Marines missing.
The search was officially called off around 3 a.m., local time, with the Navy and Marine Corps switching their focus to recovery efforts, according to a statement sent by the Expeditionary Force to the New York Times.
Next-of-kin for the three missing Marines have been notified, the military said.
There's been no word from the US President yet, but the White House said he'd been briefed on the incident.
The incident took place off the coast of Shoalwater Bay, in Australia's northeastern state of Queensland, the Australian defence ministry said.
The recent joint military exercise took place largely in Shoalwater Bay and involved more than 30,000 USA and Australian personnel, according to Australian Defense Department.
Small boats and aircraft from the 31st Marine Expeditionary Unit and Bonhomme Richard Expeditionary Strike Group searched for the missing, the Marine Corps said.
USA defense officials have not released specifics about what caused the aircraft to go down, saying only that the incident is under investigation.
'Please keep the families of those involved in the Osprey mishap near Australia in your thoughts and prayers, ' Marine Corps Commandant Robert Neller said.
According to the ABC, the tilt-rotor MV-22 Osprey had been in Queensland as part of the Talisman Sabre joint training exercise between Australian and USA forces.
The Osprey is a tiltrotor aircraft with helicopter and plane capabilities.
During a United States counter-terrorism operation in Yemen, two soldiers were reportedly injured when a USMC MV-22 experienced a "hard landing" after being called in to evacuate injured troops. Last December, a US military Osprey crash-landed off Japan's southern island of Okinawa. She also had spoken with U.S. Defense Secretary James Mattis to offer Australia's assistance, she said.
The military training exercise was held in Shoalwater Bay.