Japanese and American officials said they had so far found two of the seven Marines who had been aboard the aircraft, an F/A-18 Hornet fighter jet and a KC-130 Hercules.
“One of the recovered Marines is in fair condition and the other has been declared deceased by competent medical personnel,” a U.S. Marine Corps statement said.
The deadly crash is the latest in a string of U.S. military aviation accidents around the world in recent years, which have prompted hearings and criticism in Congress over aircraft safety.
U.S. President Donald Trump expressed gratitude to Japan for its quick assistance with search and rescue efforts.
“My thoughts and prayers are with the @USMC (U.S. Marine Corps) crew members who were involved in a mid-air collision off the coast of Japan,” he tweeted.
The incident occurred around 2 a.m. local time in Japan (1700 GMT Wednesday) about 320 km (200 miles) off the Japanese coast. The Marine Corps said the aircraft were conducting routine training at the time, including refueling training.
The U.S. military did not speculate on the cause of the collision.
“The incident is regrettable, but our focus at the moment is on search and rescue,” Japanese Defense Minister Takeshi Iwaya told a news conference. “Japan will respond appropriately once the details of the incident are uncovered.”
A U.S. Navy P-8A patrol and surveillance aircraft was helping in search and rescue efforts along with Japanese authorities, the Marine Corps said, adding that the incident was under investigation.