U.S. officials, speaking on condition of anonymity to Reuters, said one of the aircraft was an F/A 18 fighter jet while the other was a KC-130 refuelling aircraft, with a combined total of seven personnel aboard.
The aircraft are a KC-130 refuelling plane and an F/A-18 Hornet fighter jet.
Japanese search-and-rescue aircraft immediately responded to the emergency, the statement added.
Japan's Defense Ministry said the two aircraft carrying seven crew members altogether had collided midair and crashed into the sea about 100 kilometers south of the Muroto cape in Kochi Prefecture.
The statement concluded by saying that "the investigation is ongoing" and "no other information is yet available".
A total of seven personnel were believed to be on board the two aircraft, according to ABC News' Elizabeth McLaughlin.
UPDATE: This story was updated at 5:45 P.M. on December 5 after one of the missing Marines was found alive.
An FA-18, like the one shown here in Australia, was identified as one of the planes that was involved in a mishap off the coast of Japan on Wednesday.