The US Marines suspended flights of their Osprey aircraft in Japan on Wednesday as anger mounts over an accident that saw one of the hybrid planes crash off the southern island of Okinawa.

The incident came at a delicate time, with Tokyo and Washington pushing to build a new airbase on Okinawa despite local opposition against the heavy US military presence there and concerns by residents about the Osprey.

The MV-22 Osprey, a so-called tiltrotor plane that can carry 24 troops, is half helicopter half turboprop and boasts the manoeuvrability of a chopper and the speed and range of a fixed-wing aircraft.

But a series of accidents mostly in the United States involving the plane have prompted protests by Okinawa residents.

The crash happened overnight after the aircraft damaged one of its propellers during an aerial refuelling drill with another plane around 10 pm Tuesday (1300 GMT), according to Marine Lieutenant General Lawrence Nicholson.

The Osprey pilot guided the violently shaking aircraft to shallow waters near US Marine base Camp Schwab, and conducted "a controlled landing" in the water to reduce injuries to crew and avoid flying over Okinawan residential areas, he told reporters.

Nicholson said that investigations were under way and flights would not resume until he was satisfied with the results of the reviews.

He stressed, however, that the incident was not due to a mechanical problem with the aircraft.

"We apologise to Okinawan people, who perhaps will lose faith and confidence in the Osprey based on this accident," he said.

"I hope that they will not."

Japanese public broadcaster NHK showed the main wings of the craft broken in half and the cockpit separated from partially submerged fuselage.

Of the five crew members aboard, one needed "a few more days" of medical attention, one suffered a broken bone and the other three did not require serious attention, Nicholson said.

The incident quickly sparked anger on Okinawa -- a strategic outpost of US military power -- where the local governor has spearheaded a campaign against the presence of US bases, while in Tokyo the government demanded the halt to flights, which the Marines later announced.

Japanese Prime Minister Shinzo Abe called the accident "serious" and "regrettable", while Okinawa governor Takeshi Onaga, an outspoken critic of the US military presence, called the incident "really outrageous".

The accident came as Japanese media reported that another Osprey landed on its fuselage late Tuesday at Futenma airbase, located in a crowded Okinawan residential district.

The US military told the Japanese government that the plane had trouble deploying its landing gear, chief government spokesman Yoshihide Suga told reporters.

Tokyo and Washington want to move the Futenma base to a sparsely populated area in the north of the island, but many locals, including Onaga, want it removed altogether.

More than half the approximately 47,000 American troops in Japan under a decades-long security alliance are stationed on Okinawa, the site of a major World War II battle that was followed by a 27-year US occupation of the island.