Yoshitaka Shindo, minister for internal affairs and communications, paid homage this morning at the Yasukuni shrine, Jiji Press and other news reports said.
Shindo, a regular visitor to the shrine, insisted that it was a "private matter", playing down the potential for diplomatic fallout from a visit by a member of the government.
"Offering condolences to the war dead can be seen in any country," Shindo was quoted by Jiji as saying following his visit, which came ahead of the shrine's annual spring festival on April 21 to 23.
The shrine, which used to be run by the wartime government, honours Japan's war dead including several high-level officials executed for war crimes after World War II.
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China and South Korea see it as a brutal reminder of Tokyo's imperialist past and wartime aggression, and its failure to repent for its history.
In December, Prime Minister Shinzo Abe made his first visit as premier to the shrine since he took office in December 2012.
Abe's visit -- which came at a time when Japan's ties with China have turned particularly sour over a territorial dispute regarding islands in the East China Sea -- prompted an angry reaction from Beijing.
Earlier in the day, three Chinese government ships entered the territorial waters around the East China Sea islands, called the Senkaku in Japan and the Diaoyu in China, for several hours today, according to the Japanese coastguard.
Seoul also reacted angrily to Abe's visit to the shrine, while Japan's ally the United States said it was "disappointed" by the prime minister's decision as it would raise regional tensions.