The ritual-bound process began Tuesday morning with the emperor, dressed in expansive golden-brown robes and a towering black headpiece, "reporting" his abdication to his ancestors and the gods at several "sanctuaries" at the palace.
Naruhito has promised to emulate his father in seeking peace and staying close to people.
Naruhito also received messages from President Donald Trump and China's President Xi Jinping.
He said he will "reflect deeply" on the path trodden by Akihito and past emperors, and promised to abide by the Constitution to fulfill his responsibility as a national symbol while "always turning my thoughts to the people and standing with them".
"The curtain has gone up on a new era that will be filled with hope", said Hiroshi Takahashi, 78, outside his "wagashi" traditional Japanese candies shop.
Emperor Naruhito ascended the throne after his father, now-Emperor Emeritus Akihito, abdicated.
Like his popular father, he has warned of the need to remember World War II "correctly", without downplaying Japan's early 20th-century militarism.
Indonesian Foreign Minister Retno Marsudi also congratulated Emperor Naruhito on his ascension, while expressing deep appreciation for former Emperor Akihito on his abdication.
After that, female royalty will enter the room and Naruhito will make his first public remarks as emperor.
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Couples took photos at a special booth decorated with the era name Reiwa, or "beautiful harmony", for memorabilia.
Interestingly, next in line for the Japanese throne is not Crown Prince Naruhito's daughter Aiko but Naruhito's brother, Akishino' son, nine-year old Hisahito.
Thirteen adults of the Imperial family, including the Empress, Crown Prince Akishino and his wife Crown Princess Kiko, participated in the Sokui-go-Choken-no-gi, which started at 11:12 a.m. "I'm sure that further boosting of Russian-Japanese cooperation in various areas meets core interests of our peoples and is in the framework of strengthening global stability and security", the telegram says.
After that comes 83-year-old Prince Hitachi, younger brother to Akihito, who abdicated as Emperor on Tuesday. The reign of each Emperor is given a name, or gengo, which is used with the Western calendar to mark years.
The high standard of living will also likely continue - notwithstanding the fact that the Japanese economy has not grown for the past three decades. After the ratification of Japan's post-WWII constitution, the position became largely symbolic and offers no political power. Empress Emeritus Michiko was born a commoner and was Catholic educated.
In an annual news conference marking his February 23 birthday, Naruhito said he was open to taking up a new role that "suits the times".
"We hope to build the "golden age" for Philippines-Japan strategic partnership during the reign of the new emperor", he said.
Some scholars, like Jun Okumura (奧村純) at Meiji University, suggest that Naruhito's first address as monarch confirm that he is opposed to constitutional revisionism, and finds himself at odds with the conservative cabinet of Prime Minister Shinzo Abe.