A US defence official told AFP that there had been a crash after the plane took off from Marine Corps Air Station Iwakuni in southern Japan.
A spokesman for Japan's Self-Defence Forces said one of the airmen had been rescued but the immediate fate of the remaining crew members was unclear.
The crew member was being assessed by doctors, the Marine statement said, adding that "the search and rescue operations continue for the remaining six."
The C-130 was thought to be carrying five servicemen and the F-18 two, said the Japanese official, who added that Japan had scrambled four aircraft and three ships in the search.
US media also reported five crew on the C-130 and two on the F-18.
The circumstances of the mishap are currently under investigation, the military added.
In November, a US navy fighter jet crashed into the sea off Japan's southern island of Okinawa and its two crew members were rescued alive.
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 US bases.
(With inputs from agencies.)