The F-15C Eagle jet, from Kadena Air Base in Okinawan, was taking part in a routine training mission when the pilot was forced to eject before the aircraft plunged into the sea.
"I would like to personally thank the Naha Rescue Squadron for their quick response this morning, which led to the safe recovery of our airman", said Col. Richard Tanner, 18th Wing vice commander, in a statement. The jet reportedly took off from Kadena Air Base in Okinawa and crashed some 80 kilometers (50 miles) from the coast.
"I sincerely appreciate the strong support of our Japanese partners in this hard situation", he said in an 18th Wing statement issued Monday evening.More news: Air Force Captain Found 35 Years After Disappearing
It is the 12th United States military aircraft crash so far this year.
A series of accidents involving US military aircraft have stoked tensions and in January US Defence Secretary James Mattis apologised to his Japanese counterpart over the incidents.
"Accidents of USA military aircraft are occurring repeatedly", he said, according to the Kyodo news agency.More news: Why Italy has closed its ports to a migrant rescue ship
The U.S. has a heavy military presence in Okinawa that has been the source of friction with the local government and some residents.
Okinawa's anti-base Gov. Takeshi Onaga called such incidents a threat to Okinawa's future, according to the Kyodo report.
"If that happens, we can not fulfill our responsibilities to our children and grandchildren", Onaga said. The Air Force has launched an investigation following the accident.More news: E3 2018: Halo Infinite revealed, but what is it?
Japan's Self-Defense Force's F-15 fighter jets (top and 2nd from top) conduct an air exercise with U.S. Navy F/A 18 Hornet aircrafts in the skies above the Sea of Japan, Japan, in this photo released by the Air Staff Office of the Defense Ministry of Japan Nov. 13, 2017.