The planes involved were an F-18 fighter and a C-130 tanker, the official said.
Search and rescue operations were underway following a "mishap." The planes "were conducting regularly scheduled training when the mishap occurred," the statement said.
US media reported five crew were on the C-130 and two on the F-18.
Second Lieutenant Alyssa Morales, a spokeswoman for the 1st Marine Aircraft Wing based in Okinawa, told military news site Task and Purpose that one of the Marines had been rescued alive, but this could not be immediately confirmed.
The US military has about 50,000 troops stationed in Japan.
(With inputs from agencies.)