The U.S. military said the mishap occurred during a routine training mission off the shores of Yakushima Island, about 1,040 km (650 miles) southwest of the capital Tokyo.
Another Osprey thought to have been travelling with the crashed aircraft landed safely at the island's airport on Wednesday afternoon, a spokesperson for the local government said.
Japan, which also operates Osprey aircraft, said on Wednesday it had asked the U.S. military to investigate the crash.
The deployment of the hybrid aircraft in Japan has been controversial, with critics saying it is prone to accidents.
In August, a U.S. Osprey crashed off the coast of northern Australia while transporting troops during a routine military exercise, killing three U.S. Marines.
Persons:
Kiyoshi Takenaka, Tim Kelly, Kantaro, Idrees Ali, Phil Stewart, John Geddie, David Dolan, Gerry Doyle, Nick Macfie, Deepa Babington
Organizations:
Japan Coast Guard, Yakushima Fisheries Cooperative, . Air Force Special, Command, United, ., Boeing, Bell Helicopter, U.S . Air Force, Marines, Navy, Japan Self - Defense Forces, Osprey, U.S, Thomson
Locations:
Kagoshima prefecture, Japan, TOKYO, U.S, Yakushima, Tokyo, Japan's, United States, Taiwan, Okinawa, Australia