New Empress Masako, 55, and other imperial family members attended the ceremony along with Cabinet ministers, including Prime Minister Shinzo Abe, and representatives of local governments.
During the special ritual in the palace's Matsu-no-Ma state room, an nearly exclusively male audience saw Naruhito, 59, take possession of royal regalia and seals, including a sacred sword, that offers ceremonial proof of his ascension.
"In accordance with the constitution, I vow to fulfill my responsibilities as a symbol to the nation and the people of Japan", said Naruhito, the first emperor born after World War Two. All the items used in the ceremony were duplicates, as the real objects are kept in shrines around the country and are never seen.
Nevertheless, Japan festively celebrated an imperial succession prompted by retirement rather than death.
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Naruhito succeeded to the Chrysanthemum Throne at midnight after Emperor Emeritus Akihito retired the previous day.
As the representative of the people, Abe gave a speech to express congratulations to the Emperor, the symbol of the state, and said that he will "create an era in which culture is born and grows among people who care for each other in a handsome manner".
Naruhito will receive the Imperial regalia of sword and jewel as proof of succession at the ceremony Wednesday and later will make his first address.
Naruhito waves as he arrives at the Imperial Palace in Tokyo on the morning of May 1 to formally take over the Chrysanthemum Throne, following his father's historic abdication from the world's oldest monarchy.
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As CBS News senior foreign correspondent Elizabeth Palmer reported on Wednesday, Naruhito is widely expected to continue the work of his father; humanizing the emperor's role, as well as pressing for modern reforms to normalize life for the royal family.
His enthronement Wednesday marks the official start of the "Reiwa" ("Beautiful Harmony") imperial era, but is the continuation of an unbroken dynastic line that stretches back 14 centuries.
South Korean President Moon Jae-in also sent salutations, urging Naruhito to remember "pain from the war" and contribute to peace like his father.
Entrepreneurs have sold everything from "Reiwa" bottles of sake to $10 cans of air from the "Heisei" era of Akihito's reign. But much will depend on her health, since she has been recovering from what the palace describes as stress-induced depression for about 15 years. Masako has expressed an interest in topics related to children in trouble or living in poverty. Unlike many other news organizations, we have not put up a paywall.
Masako was educated at Harvard and Oxford and had a promising career as a diplomat before her marriage.
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The role was redefined by Emperor Akihito, who helped fix the damage to Japan's reputation after the war.