It added the pilot successfully ejected and was recovered.
The US Air Force F15 jet came down into waters about 80 km south of Naha, near Okinawa, at around 6.40am local time, Japan's ministry of defence has confirmed.
The pilot remained in contact with the rescuers after ejecting himself from the plane and was rescued.
GETTY ACCIDENT The pilot has been rushed to hospital with a broken leg
It is the 12th U.S. military aircraft crash so far this year.
The U.S. military has launched an investigation into the crash. It occurred during a "routine training mission", the Air Force said.
Residents of Okinawa, which hosts the bulk of American troops in Japan, have protested against the deployment of Ospreys because of repeated accidents.
After Monday's incident, Japanese Defense Minister Itsunori Onodera once again called on the USA military to ensure the safety of its aircraft and prevent future occurrences. "Accidents involving United States military aircraft are occurring repeatedly".
Okinawa hosts the bulk of USA military facilities in Japan and the accident is likely to renew concerns among residents about the safety of US military aircraft. "We would like to continue asking for their flight safety", said Itsunori Onodera, Japan's defense minister, to Japanese wire service Kyodo on Monday. "I don't think there is a country like this among developed nations".
Okinawa Governor Takeshi Onaga also criticized the Japanese government, noting that a number of troubles with US military aircraft have been reported over the past year.
An F-15 also crashed into the sea off Okinawa in May 2013.