It is understood 23 of the 26 personnel on board had been accounted for.
A search and rescue effort is under way, with boats and warships searching for the missing personnel.
Four Bell-Boeing MV-22 Osprey aircraft were in Australia from US Marine Medium Tiltrotor Squadron 268, landing in Darwin at the end of April.
Sources told The Sunday Mail one seriously injured marine was being transported to Rockhampton Hospital.
There are no Australians involved.
The Prime Minister Malcolm Turnbull was travelling back from Western Australia but his office had been briefed on the incident.
It's understood most of those rescued had serious injuries.
The strange-looking aircraft, resembling a cross between a helicopter and airplane, has capabilities including taking off vertically and travelling much faster than a helicopter.
In a statement tonight, the US Military said: "The United States Marine Corps confirms there is an active search and rescue operation ongoing for service members involved in an MV-22 mishap off the east coast of Australia. Ship's small boats and aircraft from the 31st Marine
Expeditionary Unit and Bonhomme Richard Expeditionary Strike Group are conducting the search and rescue operations. We will provide more details as they become available."
n a statement, federal Defence Minister Marise Payne has confirmed that no Australian Defence Force personnel were on board the aircraft.
"I have been advised of an incident involving a United States Marine Corps MV-22 Osprey helicopter off the coast of Shoalwater Bay today.
"The United States are leading the search and recovery effort.
"I have briefed Prime Minister Turnbull and spoken with Secretary Mattis this evening to offer Australia's support in anyway that can be of assistance."
"Our thoughts are with the crew and the families affected".
The 31st Marine Expeditionary Unit shared photos of an Osprey helicopter conducting amphibious training from the USS Bonhomme Richard off the coast of Shoalwater Bay yesterday.
