Japanese Defense Minister Takeshi Iwaya said that the MoD "will put all our efforts to save the life [of the pilot] first", according to The Japan Times.
The previous four aircraft had been used for training in the United States before being brought to Japan, the defense official said. The missing jet was reportedly the first F-35A assembled at the Mitsubishi Heavy Industries facility in Nagoya.
Early, Japanese national broadcaster NHK has reported that Japan Air Self-Defence Force F-35A has disappeared from radar screens during a routine training flight.
Despite troubling reports in recent months about the F-35s operational readiness, only one other F-35 has been lost thus far.
The ASDF's radar lost track of the jet when it was about 135 km east of Misawa Air Base in the prefecture, Japan Times reported. The pilot had 3,200 hours of flight time, with 60 hours on the F-35, the official said. The U.S. Air Force, Navy and Marine Corps all have versions of the F-35.
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Iwaya says 12 other F-35s at the Misawa base will be grounded.
The Pentagon said it was monitoring the situation. It was also the first crash of an A version of the fifth-generation fighter, which is created to penetrate enemy defenses by evading radar detection.
The first crash, of an F-35B, occurred in SC in September 2018, which led to a temporary grounding of all F-35 aircraft to inspect "suspect fuel tubes" that may have been a factor in that incident.
The F-35C model is the US Navy's version, designed for use off its aircraft carriers.
Japan has started deploying the expensive USA -made F-35s since last year, part of its plan to bolster its defense spending and weapons capability in the coming years to counter potential threats from North Korea and China.