The Kyodo news agency said the jet belonged to the US Kadena Air Base and crashed early Monday morning about 80 kilometres south of Naha, the regional capital of Japan's southern Okinawa island.
"Our hearts and prayers go to the pilot and his family as they go through this hard time", a post said.
The pilot of an F-15C Eagle from Kadena Air Base "successfully ejected and was safely recovered" by the crew of a Japan Air Self-Defense Force helicopter, according to statements from the Air Force and the Okinawa Defense Bureau.
After Monday's incident, Japanese Defense Minister Itsunori Onodera once again called on the US military to ensure the safety of its aircraft and prevent future occurrences.
The cause of the mishap is unknown, the wing statement said.
The pilot of the fourth-generation aircraft was conducting a routine training flight when the crash occurred over the southern waters of Okinawa. "We will continue asking them to ensure safety", he said.
"I will ask for detailed reports about why it happened", he added.More news: Singapore summit: Will striking a deal with Trump risk Kim's regime?
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The aircraft was conducting a routine training mission with six other F-15 fighters at the time, and the pilot, the sole person on board, was ejected, according to the U.S. military and the ASDF. The pilot remained in contact with the rescuers after ejecting himself from the plane and was rescued.
The U.S. Air Force is also considering replacing the F-15s, worth around $36 million each, with F-16 fighting falcons by 2020.
The Okinawa government asked the United States military to suspend F-15 flights until they are confirmed safe, while the prefectural government and local towns hosting the base are set to lodge protests against the USA military.
"If that happens, we can not fulfill our responsibilities to our children and grandchildren", Onaga said.
An F-15 fighter crashed into the sea off Okinawa in May 2013, and an object weighing 1.4kg fell off an F-15 fighter during a flight in February.
The Japanese government is therefore moving ahead with the plan to relocate the airbase from an urban area in central Okinawa to the less populated Henoko district.