Economy minister Yasutoshi Nishimura visited Tokyo's war-linked Yasukuni Shrine on Monday, a day before its autumn festival.
After offering prayers at the shrine, which honors convicted war criminals along with the war dead, Nishimura told reporters he made a ritual offering, paid for out of his own pocket.
"I prayed for the spirits of those who died in war to rest in peace, with the country and families in mind," the economy, trade and industry minister said.
Past visits by Japanese leaders and lawmakers to the Shinto shrine have riled Japan's Asian neighbors, as they view it as a symbol of the country's past militarism.
In an apparent attempt to avoid confrontation with China and South Korea, recent Japanese prime ministers have only sent offerings to the shrine for its biannual festivals in spring and autumn, as well as on the anniversary of Japan's surrender in World War II on Aug. 15.