Japanese Defence Minister Tomomi Inada, who accompanied Prime Minister Shinzo Abe to Pearl Harbour where he made an anti-war proclamation, visited the controversial shrine for the war dead on Thursday.
Japanese leaders' visits to the famous shrine is seen unfavorably in neighboring China and South Korea which suffered under Japanese imperialism.
Television footage showed Inada entering the shrine wearing a black jacket and a smile on her face, Reuters reported.
South Korea said the defence minister's trip to the shrine, which is seen as a symbol of Japan's militarism and wartime atrocities, was "deplorable".
"We express deep concern and regret over Japan's defence minister visiting Yasukuni Shrine, even as our government has been emphasising the need to create a new, forward-looking South Korea-Japan relationship," South Korea's defence ministry said in a statement.
"It's beyond deplorable that a responsible Japanese politician would worship at Yasukuni Shrine, which beautifies past colonial invasion and aggression war, and enshrines war criminals," the statement added.
It was Inada's first visit to Yasukuni as defence minister, after assuming office in August. "I visited the shrine wishing to firmly create peace for Japan and the world from a future-oriented perspective," the hawkish politician said, according to Reuters.
"Whatever historical view one may have, any country would understand the act of expressing appreciation and tribute to those who sacrificed their lives for their own country," added Inada, who is known for her strong nationalistic views.
On Tuesday Inada joined Abe and US President Barack Obama in Pearl Harbour to pay respects to the victims of the Japanese bombing 75 years ago.
"I offer my sincere and everlasting condolences to the souls of those who lost their lives here, as well as to the spirits of all the brave men and women whose lives were taken by a war that commenced in this very place," Abe said in Pearl Harbour.