Chief Cabinet Secretary Yoshihide Suga in a statement said the exception to exporting Japanese parts was made as the United States, leading the F-35 program, will "strictly" control shipments, Kyodo News reported.
Under the current ban put into effect in 1967, Japan does not permit exports of weapons to communist nations, countries subject to U.N. Security Council embargoes, or those involved in international conflicts.
Questions about the F-35 exception, however, could come up when Israel buys the stealth fighters with Japan-made parts, Kyodo reported.
U.S. aircraft maker Lockheed Martin Corp. is the leader of the international consortium involved in the F-35 program.
Suga's statement said Japan would continue to uphold its "basic principle of being a pacifist nation" and that participation in the project by Japanese companies would help "maintain, nurture and upgrade the basis of our country's production of defense material and its related technology."
Japan plans to buy four F-35s by 2016 and eventually have 42 of them for the country's Air Self-Defense Force, Kyodo said.
Previous exceptions to the ban have included supply of weapons technology and production of missile defense systems with the United States.
The Asahi Shimbun reported Japanese Prime Minister Shinzo Abe's administration had making and exporting F-35 parts will not be against its interpretation of guidelines banning weapon sales that could "exacerbate international conflicts."