Defense Minister Takeshi Iwaya told reporters that a search and rescue operation was underway for the missing jet and its pilot.
The plane lost contact about 30 minutes after taking off from Misawa Air Base, public broadcaster NHK said.
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.
13 F-35A are now based at Misawa AB, based on Japanese media reports.
JASDF aircraft, along with Japan Maritime Self Defense Force (JMSDF) and Japan Coast Guard (JCG) vessels, have begun a search mission.
The Japanese F-35 fighter jet missing in the Pacific could be a major security headache for the USA if Russian Federation or China locate the state-of-the-art fighter jet first, experts warn. The first one occurred on September 28, 2018 when a U.S. Marine F-35B Lightning II crashed near Beaufort, South Carolina.
Officials said there was no known problem with the aircraft before contact was lost, but the 12 other F-35As have been grounded at the Misawa Air Base in the wake of the crash. Lockheed Martin also makes a C version of the fighter created to operate off carriers.
Japan is deploying F-35As, each of which costs more than 10 billion yen ($90m), to replace the ageing F-4 fighter jet.
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.
The U.S. military temporarily grounded its entire fleet of F-35s a year ago after one of the jets crashed during a training mission in SC.
In the Pacific, South Korea and Australia have joined Japan in acquiring the jets.