The planes involved are a KC-130 and an F/A 18, carrying a total of seven personnel, USA media quoted officials as saying. Search and rescue operations were underway at the scene.
USA media also reported 5 crew on the C-130 and 2 on the F-18.
The circumstances of the mishap were under investigation and no other information was available, according to the statement.
It was unclear if U.S. military officials were also assisting with the search. Japanese search and rescue aircraft were immediately deployed and rescued at least one Marine.
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"The aircraft involved in the mishap had launched from Marine Corps Air Station Iwakuni and were conducting regularly scheduled training when the mishap occurred", the Marine Corps Base Camp Butler statement read.
A Marine Corps KC-130 aerial tanker and an F/A-18 Hornet have crashed off Japan, a defense official told Task & Purpose on Wednesday.
Those incidents have stoked tensions between close military allies Washington and Tokyo and led to protests against the deployment of Ospreys by residents living near United States bases.