Both aircraft are reported to have crashed into the water.
The Marine Corps said in a statement the incident occurred around 2 a.m. local time in Japan (1700 GMT Wednesday) about 200 miles (322 km) off the Japanese coast. The aircraft - an F/A-18 Hornet and a KC-130 Hercules - were involved in "regularly scheduled training" at the time, and Japanese authorities immediately launched search-and-rescue aircraft afterward.
The U.S. military's III Marine Expeditionary Force, headquartered in Okinawa Prefecture, voiced gratitude to the MSDF for their help.
Japanese officials said two crew members were in the F/A-18, and five others in the KC-130.
The KC-130 is an extended-range tanker version of the C-130 and is used for mid-air refuelling.
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Search and rescue operations are underway.
They also said they were unsure how the mishap may have occurred but none suspected foul play.
A Marine spokesman released a statement saying one of the personnel from the planes "is being evaluated by competent medical authorities".
The BBC's Rupert Wingfield-Hayes in Tokyo says that air-to-air refuelling is a hard and potentially risky flight operation, especially when done at night.
More than 50,000 U.S. troops are based in Japan under the bilateral security pact.