The US Marine Corps said in a short statement that the incident occurred at 2 am local time on Thursday some 320 kilometers (200 miles) off the coast of Japan.
It said a combined total of seven personnel were aboard the two aircraft and only one had been rescued so far.
The aircraft had launched from Marine Corps Air Station Iwakuni and were conducting regular training when there was a "mishap," the Marine Corps said.
A US official, speaking on condition of anonymity, said one of the aircraft was an F/A 18 fighter jet, while the other was a KC-130 refueling aircraft.
Japanese officials said two crew members were in the F/A-18, and five others in the KC-130.
Japan's defense ministry said that its maritime forces had rescued one person and search and rescue efforts are ongoing.
US officials who spoke on condition of anonymity were unsure how the mishap may have occurred but none suspected foul play. An investigation has begun.
The crash is the latest in recent series of accidents involving the US military deployed to and near Japan.
Last month, a US Navy F/A-18 Hornet from the aircraft carrier USS Ronald Reagan crashed into the sea southwest of Japan’s southern island of Okinawa, though its two pilots were rescued safely.
In mid-October, a MH-60 Seahawk also belonging to the same aircraft carrier crashed off the Philippine Sea shortly after takeoff, causing non-fatal injuries to a dozen sailors.
More than 50,000 US troops are based in Japan under the bilateral security pact.
Pacifist inclinations as well as security and safety concerns have prompted the Japanese to protest against the US military presence in Japan from time to time.
Multiple cases of misconduct by US forces have also raised anti-American sentiment among the islanders.