U.S. media say the two planes crashed during midair refuelling but this has not been officially confirmed.
The Maritime Self-Defence Force, which dispatched aircraft and vessels to join in the search operation, said Japanese rescuers found one of the crew members in stable condition.
Japanese search-and-rescue aircraft immediately responded to the emergency, the Marine Corps statement said.
A U.S. official, speaking on condition of anonymity, said it occurred during a refueling exercise.
The Marines refuel aircraft differently to the Air Force, said Carl Baker, executive director of the Pacific Forum think tank in Hawaii.
Luke MilanoUS Marines Launch Search and Rescue Effort After Two Planes Crash Near Japan
A KC-130 midair refueling a tanker and an F/A-18 fighter jet, which was being refueled, were involved in what the military called a "mishap".
The aircraft are based in the US Marine Corps base in Iwakuni, west of Hiroshima.
It said in a statement that the accident is under investigation and gave no further details.
In November, a U.S. navy fighter jet crashed into the sea off Japan's southern island of Okinawa and its 2 crew members were rescued alive.
And in mid-October, an MH-60 Seahawk belonging to the same carrier crashed off the Philippine Sea after takeoff.