Senior Vice Foreign Minister Nobuo Kishi, the younger brother of Prime Minister Shinzo Abe, visited the war-linked Yasukuni Shrine on Saturday during its annual autumn festival.
After paying homage at the shrine during the four-day festival through Sunday, Kishi told reporters he entered his name in the register book with a title as House of Representatives member.
He said his visit would not have an impact on Japan's relations with other countries and that he had not conferred with the prime minister about the visit.
The shrine is seen by some countries as a symbol of Japan's past militarism as it honors convicted Class-A war criminals along with Japan's war dead.
Abe told reporters later in the day, "I said in the past that it was extremely regrettable I could not visit the shrine during my previous stint (as prime minister), and I still have the same feeling."
On Friday, Internal Affairs and Communications Minister Yoshitaka Shindo and a cross-party group of 157 lawmakers visited the shrine, drawing criticism from China and South Korea.
Abe himself offered a "masakaki" tree, traditionally used in Shinto rituals, to the shrine on Thursday but did not make a visit in an apparent bid to not further aggravate ties with Beijing and Seoul.