Yoshitaka Shindo, minister for internal affairs and communications, insisted he was paying homage at Yasukuni Shrine as an individual, and played down the potential for diplomatic fallout.
"I offered prayers in a private capacity," Shindo, who wore a morning suit, told reporters after making his offering of a branch from a sacred tree.
"I mourned people who lost their lives in wars and prayed for peace," said Shindo, whose grandfather, the commandant of a garrison on Iwojima, died in the infamous battle for the island.
Asked if his visit to the shrine would affect Tokyo's ties with other Asian countries, he said: "It's not something that should provoke comments from anyone."
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"I don't think this will develop into a diplomatic issue at all."
The visits were part of the autumn festival at Yasukuni, which runs until Sunday. Thousands of veterans from WWII or their bereaved families are expected to pay homage, while tourists, both domestic and foreign, will also visit.
Prime Minister Shinzo Abe yesterday donated a symbolic gift to the shrine, in what was taken as a sign that he would not be visiting.
It is controversial because of the inclusion of 14 of the men held responsible for Japan's often-brutal behaviour as it invaded a swathe of Asia in the 1930s and 1940s.
In addition, the museum that is attached to the shrine peddles a largely unapologetic view of WWII that is not widely accepted, either at home or abroad.
China and South Korea, whose peoples suffered under Japan's militarist rule, say Yasukuni is a symbol of Tokyo's present-day unwillingness to come to terms with its past misdeeds.
Nationalists, among them a significant number of parliamentarians, visit the shrine in spring and autumn, as well as on August 15, the anniversary of Japan's WWII surrender.