The incident is under investigation, the Marine Corps said.
The Marine Corps suggested Japanese search and rescue aircraft had taken the lead on the rescue mission.
Six US marines were missing after 2 American military aircraft crashed on Thursday during a refueling operation off the coast of Japan, officials from both countries told AFP.
They also said they were unsure how the mishap may have occurred but none suspected foul play.
The Marines refuel aircraft differently to the Air Force, said Carl Baker, executive director of the Pacific Forum think tank in Hawaii. A United States official, speaking on condition of anonymity, said it occurred during a refuelling exercise.
The fate of the planes and service members aboard was not immediately clear.
Luke MilanoUS Marines Launch Search and Rescue Effort After Two Planes Crash Near Japan
"The incident is regrettable, but our focus at the moment is on search and rescue", he said.
No other details were provided.
A Marine Fighter Attack Squadron 224 F/A-18 Hornet conducts an aerial refuel utilizing a KC-130J in coorlation with Weapons and Tactics Instructor Course in Yuma, Ariz., April 10.
The aircraft are based in the US Marine Corps base in Iwakuni, west of Hiroshima.
The crash comes just a month after a US F/A-18 Hornet from the aircraft carrier USS Ronald Reagan crashed into the sea southwest of Okinawa.
More than 50,000 USA troops are based in Japan under the bilateral security pact.More news: Soybeans Lead Gains in Agriculture on U.S.-China Trade Truce