Speaking to reporters, Japanese Defense Minister Takeshi Iwaya said the JASDF will ground the 12 remaining F-35As for the time being. The aircraft lost had a total of 280 flight hours prior to the crash.
Search operations by the Self-Defense Forces and the Japan Coast Guard are continuing.
Japan began deploying F-35As, costing more than 10 billion yen ($90 million) each, in January previous year, to replace the aging F-4 model.
"In December 2018, the Japan Ministry of Defense announced its decision to increase its procurement of F-35s from 42 to 147".
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Japanese defense officials said a search was underway for an F-35 fighter jet after the state-of-the-art aircraft disappeared from radar during a flight exercise in northern Japan on Tuesday.
Japan's military has reportedly found what appears to be debris from the F-35A fighter jet that disappeared from radar with one pilot on board during a training mission over the Pacific Ocean on Tuesday evening.
The aircraft crashed in waters that reach a depth of around 1,500 metres, making recovery, particularly of the aircraft's flight data recorder (FDR), difficult, the official said.
"The current unit price of the F-35 ranges from US$90 million (S$122 million) to US$115 million per aircraft, comparable to what we have paid for our F-15SGs", he revealed.
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The country's Air Self-Defense Force said the stealth jet, an F-35A model, went missing while flying off the eastern coast of Aomori.
United Kingdom officials are in close touch with the U.S. F-35 Joint Programme Office, but there was now very little information available about the incident, the spokesperson said.
This marks the first crash of the "A" variant of the fifth-generation F-35 fighter.
Eight ships and seven aircraft, including a U.S. Navy P-8 Orion maritime patrol plane, are taking part in search and rescue efforts. An F-35A squadron with 80 personnel was formed last month at the Misawa base.
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The last time this happened the plane crashed near the Marine Corps Air Station Beaufort, South Carolina. More than 320 of the fighters operate from 15 American bases worldwide, though the Pentagon and Lockheed continue to wrestle with resolving more than 900 deficiencies - including flaws in the plane's complex software.