"I earnestly hope that the ravages of war will never again be repeated," he said at a ceremony on Saturday.
Meanwhile, Prime Minister Shinzo Abe promised to "never repeat the tragedy".
The PM marked the occasion by sending an offering to a controversial war shrine in Tokyo, but did not visit in person.
However, four ministers did visit the Yasukuni Shrine, in a move that is likely to anger China and South Korea.It is the first time in four years such senior politicians have attended the shrine, which pays homage to a number of senior figures convicted of war crimes as well as the country's war dead.
"I paid respects... to the souls of those who nobly sacrificed themselves during the war," Education Minister Koichi Hagiuda explained to reporters.
Emperor Naruhito delivered a shoot speech at a memorial service in Tokyo, which was scaled back due to the coronavirus pandemic. About 500 people were in attendance compared to more than 6,000 last year and face masks were compulsory.
"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," he said at the event.
Naruhito, 60, began his reign in May last year after his father, Emperor Akihito, became the first monarch to abdicate the throne in more than 200 years.
South Korea's President Moon Jae-in did not mention the controversial visits to the Yasukuni Shrine in remarks made on Saturday.
President Moon instead used the occasion - known as Liberation Day in South Korea - to say his government was prepared to sit down for face to face talks over historical disputes at any time.
Seoul and Tokyo are divided over compensation demands for Koreans forced to work under the Japanese occupation, which began in 1910 and ended in 1945.
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