"A total of eight airplanes were sent to the area, but we have not received any information about the fighter", the spokesman said.
There was no word yet on the fate of the pilot on board, Defence Minister Takeshi Iwaya said on Wednesday.
The Royal Australian Air Force, which has 72 planes on order, did not immediately respond to a request for comment.
The pilot, a major in his 40s, was flying with three other aircraft near Aomori prefecture when he lost contact.
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 aircraft went missing about 30 minutes after taking off from Misawa air base in northern Japan.
As of August 2018, more than 310 F-35s have been delivered to militaries around the world, according to the plane's maker, Lockheed Martin. Lockheed Martin also makes a C version of the fighter created to operate off carriers.
Lockheed said it was standing by to support the ASDF as needed.
This June, 2017, photo shows Japan Air Self-Defense Force's F-35A stealth jet at a factory of Mitsubishi Heavy Industries, in Toyoyama, central Japan.
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. The F-35A, like the one Japan lost contact with Tuesday, is the one designed for air forces to use off conventional runways.
The crash was only the second time an F-35 has gone down since the plane began flying nearly two decades ago.
The purchase affects the balance of payments between the U.S. and Japan, as the United States pushes its main allies, including South Korea and Germany, to shoulder more defense costs, including the basing of USA troops on their soil.
Japan is deploying F-35As, each of which costs more than 10 billion yen ($90m), to replace the ageing F-4 fighter jet.
Under guidelines approved in December, Prime Minister Shinzo Abe's government plans to buy 147 F-35s, including 105 F-35As, costing about $90 million each.
Japan started deploying the expensive F-35s a year ago as part of its plan to bolster defense spending and weapons capability to counter potential threats from North Korea and China.