Naruhito expressed the remorse at an annual ceremony at Nippon Budokan Hall in Tokyo to commemorate the 3.1 million Japanese who died in the war.
Prime Minister Shinzo Abe sent a ritual offering to the controversial Yasukuni Shrine.
The 59-year-old emperor, who ascended the Chrysanthemum Throne in May, was speaking against the backdrop of the 74th anniversary of the country’s World War II surrender.
He said: “Looking back on the long period of post-war peace, reflecting on our past and bearing in mind the feelings of deep remorse, I earnestly hope that the ravages of war will never again be repeated.”
The emperor, Empress Masako, Abe and at least 5,000 family members of the war attended the annual ceremony at Nippon Budokan Hall in Tokyo.
Naruhito said that he made his first appearance as emperor at the annual event “with a deep and renewed sense of sorrow”.
Abe, who is unlikely to offer prayers himself at the shrine, paid for the sacred tree branch to be sent to the war memorial, which honours the nation’s war dead, including convicted war criminals.
Dozens of conservative lawmakers paid their respects at the controversial shrine early Thursday.
Visits to the shrine by political leaders provoke anger in neighbouring countries, especially China and South Korea, which see it as glorifying Japan’s wartime aggression.
Abe has not paid homage at the shrine since Dec. 2013, when his visit sparked an international outcry.
This year’s anniversary comes amid an escalating trade dispute with South Korea.
In early July, Abe’s government imposed restrictions on South Korea-bound shipments of materials used in semiconductors and smartphone production.
On August 2, it then approved plans to remove South Korea from a white list of trusted trading partners, sparking protests from Seoul.
On Tuesday, South Korea announced its own plans to downgrade Japan’s trade status.
(Edited by Emmanuel Yashim)
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