Empress Masako sat on the adjacent throne in a layered court kimono during the ceremony.
Empress Masako attends a ceremony to proclaim Emperor Naruhito's enthronement (POOL/AFP via Getty Images)
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"I hearby proclaim to inside and outside of the country that I have enthroned," Naruhito said as he stood inside the Imperial Throne.
"I hereby swear that I will act according to the constitution and fulfill my responsibility as the symbol of the state and of the unity of the people of Japan, while always praying for the happiness of the people and the peace of the world as I always stand with the people."
Emperor Naruhito, left, delivers his speech as Empress Masako, second from left, Prime Minister Shinzo Abe, right, and other officials attend the enthronement ceremony
AP
The emperor also wore a black headdress decorated with an upright tail, appeared as a pair of black-robed chamberlains opened the purple curtains of the throne at the sound of a bell.
The enthronement ceremony was originally modelled after one by the ancient Tang dynasty of China and the second of a three-part process following the May succession. Next month sees the highly religious and divisive ritual of the Grand Harvest.
Some experts have raised questions over the government's funding of 16 billion yen ($150 million) for ceremonies that contain religious rites.
Prince Charles at the British Embassy prior to Enthronement Ceremony of Emperor Naruhito (Photo by Tim Rooke - Pool/Getty Images)
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Criticism was largely eclipsed by the festive mood, in part because Naruhito's succession was by abdication not by death, palace watchers said.
A parade originally planned for Tuesday afternoon has been postponed until Nov. 10 due to a deadly typhoon that caused flooding and other damage in central and northern Japan.
Charles' visit includes a day of engagements in Tokyo to celebrate British-Japanese connections.
Charles has been to Japan four times before and last visited in 2008. He also attended the ceremony of enthronement of Emperor Akihito in November 1990.