In December, Japan announced its plans to place an order for 105 more F-35s from the USA on top of the 42 it had already bought - a deal which would make Japan the largest global buyer of the troubled plane.
The country has now grounded its 12 remaining F-35 fighter jets at the Misawa base temporarily, said Defence Minister Takeshi Iwaya.
The accident could influence Switzerland's decision, but Finland could still pick the F-35 as it is close to Russian Federation, said Justin Bronk, a research fellow at the Royal United Services Institute in London.
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.
"We recovered the wreckage and determined it was from the F-35", a spokesman for the Air Self Defence Force (ASDF) said, adding that the pilot of the aircraft was still missing.
Japan began deploying F-35As, costing more than 10 billion yen ($90 million) each, in January a year ago, to replace the aging F-4 model.
A September crash of an F-35B - the Marine Corps model of the plane - in SC prompted the Pentagon to suspend most flights for about two weeks to inspect a fuel line investigators believed may have contributed to the incident.
No problems with the aircraft had previously been reported, according to Japan's public broadcaster NHK.
A representative for Mitsubishi Heavy Industries, who assemble the aircraft, said it had no immediate comment.
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The lost aircraft, assembled in Japan, cost 14 billion yen ($125.98 million), several million dollars more than one purchased directly from the United States.
It had only been in the air for 28 minutes before the crash on Tuesday, Japanese officials said.
According to the Defense Ministry, the missing pilot was a seasoned veteran with about 3,200 hours of flight experience including about 60 hours of flying an F-35A.
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 F-35A lost radar contact approximately 85 miles east of Misawa Air Base. The F-35 fighter jet is able to evade enemy's radar and penetrate deep into enemy's space without detection. It was also the first crash of an A version of the fifth-generation fighter, which is created to penetrate enemy defences by evading radar detection.
Lockheed Martin, which manufactures the aircraft, said it was standing by to support the Japanese Air Self Defence Force as needed.
Britain, which has 17 F-35B model jets that can take off and land vertically, has not grounded its fleet, but is monitoring the situation closely.
According to several Japanese media outlets, an F-35A Lightning II belonging to the Japan Air Self Defense Force is now reported as missing during a mission over the Pacific Ocean. A U.S. Marine Corp short take off and landing (STOVL) F-35B version crashed near the Marine Corps Air Station Beaufort in SC in September, prompting a temporary grounding of the aircraft. 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.
"If one of Japan's F-35s is sitting at the bottom of the Pacific, we are probably about to see one of the biggest underwater espionage and counter-espionage ops since the Cold War", Rogoway tweeted.