Defense Minister Tomomi Inada resigned Friday over an alleged cover-up involving Japanese peacekeepers in South Sudan, local media reported.
Prime Minister Shinzo Abe announced the resignation of his key Cabinet ally, the Kyodo news agency said.
The development came ahead of a planned Cabinet reshuffle next week designed to halt the government's steady fall in approval ratings. Inada has been expected to lose her job in the changes.
Inada, who has denied a role in the alleged cover-up of the daily activity logs of Japanese troops serving with the UN force, is the sixth minister to resign since Abe returned to office in December 2012.
Foreign Minister Fumio Kishida is to take over her duties until a new defense minister is appointed, Kyodo reported.
A Defense Ministry investigation found that the soldiers' logs showed the deteriorating security situation in South Sudan, which could have affected the government's push for continued military participation.
The probe found a series of legal violations by officials but denied that Inada helped conceal the data.
Japan has strict laws governing overseas troop deployments. Tokyo withdrew its troops from South Sudan, which is embroiled in an ongoing civil war, in May.
Inada's resignation came a day after opposition leader Renho stood down from the Democratic Party following poor results in the recent Tokyo election.
The former television presenter, who uses one name, said she did not have the ability to maintain party unity in the wake of the defeat. The Democratic Party won five of 127 seats in the Tokyo Metropolitan Assembly on July 2.
