As of midday Wednesday in Japan, the plane's pilot, reportedly in his 40s, was still missing. A Marine Corps F-35B fighter jet crashed near the Marine Corps Air Station in Beaufort, S.C., in September.
Japanese Defence Minister Takeshi Iwaya told journalists it is not clear if the F-35 crashed. The other crash involved a U.S. Air Force F-35A. "Big deal", said Tom Moore, a former U.S. Senate Foreign Relations Committee senior staff member.
It marked the first-ever crash of an F-35A fighter jet, which performs normal take-offs and landings like other planes, according to the ministry.
Iwaya said the remaining 12 F35As will be grounded for the time being and that all Air Self-Defense Force flights will be suspended throughout the day except for scrambles and certain missions such as transport.
The fighter jet went missing around 7.30pm (local time) as it was flying some 135 kilometres east of Misawa, northeastern Japan, a ministry spokeswoman said.
The US Navy (USN) has deployed an Arleigh Burke-class guided-missile destroyer, USS Stethem (63) and a P-8A maritime patrol aircraft (MPA) to assist in the Japanese-led search for a missing Japan Air Self-Defense Force (JASDF) pilot.
The aircraft was at the front of a group of four planes out for training maneuvers when it sent an "aborting practice" signal before going down.
Under guidelines approved in December, Prime Minister Shinzo Abe's government plans to buy 147 F-35s, including 105 F-35As, costing about 10 billion yen (£69 million) each.
The aircraft crashed in waters whose depth reach about 1,500 metres, making recovery, particularly of its flight data recorder, or black box, difficult, the official said.
There are now 13 F-35As deployed at the Misawa base where a new squadron has been formed with 80 personnel.
Lockheed Martin said in a statement that he was ready to support the Japanese Air Self-Defense Force as needed. It is made by Lockheed Martin, but the crashed plane is the first to be assembled in Japan by Mitsubishi Heavy Industries in Nagoya, Japan.