He declared his enthronement from the Takamikura, the Japanese imperial throne, with two of Japan’s Three Sacred Treasures – an ancient sword and a jewel – placed beside him.
The treasures, along with a mirror called Yata-no-Kagami, comprise the regalia that symbolises the legitimacy of the emperor.
Ahead of the ceremony, Japan’s government pardoned 550,000 people guilty of minor crimes like traffic violations.
Emperor Naruhito, 59, and his Harvard-educated wife Empress Masako, 55, took the throne in May following a brief traditional ceremony but today’s Ceremony of Accession is an official announcement of his new status.
The mood was dampened in the aftermath of Typhoon Hagibis which devastated Japan 10 days ago, killing at least 80 people.
A celebratory parade planned for Emperor Naruhito’s enthronement was postponed out of respect for the victims.
Nonetheless, congratulatory banners were hung at subway stations and on street corners, while small groups of people waited at the gates of the Imperial Palace to cheer the emperor as he arrived by car.
Emperor Naruhito began the day’s ceremonies by visiting his imperial ancestors at a shrine on the palace grounds, wearing a black headdress and white robes with a long train.
Empress Masako followed him later, dressed in 12-layered white robes and helped by two women to arrange her train.
The main ceremony was held at the Imperial Palace’s Matsu no ma, the most prestigious place in the palace.
The emperor wore a traditional burnt-orange robe and headdress and sat alongside Empress Masako as he read out a formal proclamation.
“I swear that I will act according to the constitution and fulfil my responsibility as the symbol of the state and of the unity of the people,” he said, according to a Reuters translation.
Prime Minister Shinzo Abe delivered a congratulatory speech, followed by shouts of “long live the emperor”.
The ceremony was attended by dignitaries from more than 180 countries, including Prince Charles.
Naruhito is the first Japanese emperor born after the Second World War, ascending to the throne after his father, Akihito, became the first Japanese monarch to abdicate in two centuries.
The former emperor worried that his age would prevent him from performing his official duties.
“It’ll be nice if the new emperor will be as kind-hearted as the former emperor and stay close to the people,” said Ryoya Suzuki, 25, in front of the palace.
Akihito pledged during his enthronement ceremony that he would observe Japan’s pacifist constitution and be a symbol of the state.
Emperor Naruhito has promised to follow in his father’s footsteps.