The F-35 stealth jet has been called the most expensive weapons system in history, and its development was beset by multiple delays before it was deemed combat ready.
Japan has 13 operational F-35s, with almost 150 more on order.
The stealth fighter, which has been beset by cost overruns and delays, has a price tag of around $100 million each.
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.
Japan's national public broadcaster, NHK, quoting Japan Air Self-Defense Force officials, reported that the missing F-35A was one of four JASDF F-35As that had taken off from nearby Misawa Air Base for a training mission at 7:00 p.m. local time.
That's about all that's know thus far, but if the plane is found to have crashed, it would be the second such incident for an F-35.
Japan's first squadron of F-35s has just become operational at the Misawa air base and the government plans to buy 87 of the stealth fighters to modernize its air defences as China's military power grows. In December, Japan announced its plans to place an order for 105 more F-35s from the U.S. on top of the 42 it had already bought - a deal which would make Japan the largest worldwide buyer of the troubled plane.
The fighter jet was flying with three others of the same make about 135km off the coast.