But not everyone is on board with the ritual, which has been criticized for violating the constitutional separation of religion and state.
Preparations for the ritual began months ago, when a turtle shell was baked until it was cracked. The cracks in the shell were then subjected to a divination act to determine the rice to be used in Daijosai should be planted, according to Japologologist John Breen, who has written about the ceremony. In this case, the rice was planted in fields in the Kyoto and Tochigi prefectures.
At the ceremony, Naruhito will offer the newly harvested rice to the sun goddess in two custom-built wooden halls in the Imperial Palace area. The halls ̵
"Daijosai transforms the emperor from just a common man into a sovereign whose authority extends to both this kingdom and the other kingdom," Breen said. "Daijosai only happens once in a reign – it is an important event. Because it involves the emperor with the sun goddess in the most intimate way, it transforms him."
About 700 people – including Prime Minister Shinzo Abe – – have been invited to attend the ceremony, although they will not enter the halls with the emperor.
Japan claims that it is the world's oldest continuous monarchy, with over 2000 years of tradition.
What happens during the ceremony?
The emperor will spend about six hours with the sun goddess in two different halls. There are various theories about what happens during the ceremony, attended only by the emperor, two "maid" and the sun goddess, Breen said.
During the 1920s, the belief that the state accepted was that the emperor had conjugal relations with the sun goddess, according to Breen. Both halls are furnished with a bed covered with a silk blanket – and the theory was that the emperor lay on the bed, covered himself with a sheet and waited for the sun goddess to come down from the sky and enter his body.  But that idea has fallen out of favor. In 1990 – when the former emperor underwent the ritual – the imperial household rejected the theory and said that the emperor did not lie on any of the beds. Instead, the beds are there to "welcome the tired sun goddess coming down from the sky," Breen said.
"There is still an important communion between the emperor and the sun goddess, and this is the essence of this Daijosai," he said.
The ceremony dates back to the 8th century, when it was created to reinforce the idea that the emperor got his right to rule from the sun goddess. "If the emperor claims the provenance of the sun goddess, then the stability of his government is so much safer," Breen said.
Until the 20th century, Japanese rulers were considered to be the living body equation of gods. Naruito's grandfather, Emperor Hirohito, was the last divine emperor.
After World War II, the United States occupied Japan. The country introduced a new constitution that banned the imperial family from engaging in politics and Emperor Hirohito renounced his divine status.
Today, Naruhito is a symbol of the state rather than the head of state, and the Japanese emperor wields no political power
What is the ?
The imperial household says that tradition is an integral part of a magician – but critics say it jeopardizes Japan's separation of religion and state.
According to Japan's constitution, the state must refrain from religious activities and cannot finance religious institutions. Critics say that Daijosai is an example of the state funding a religious ritual – and harkens back to a time when the emperor was considered to be the human embodiment of a god.
When Naruhito's father Emperor Akihito underwent the 1990 rite, a number of citizen groups began legal proceedings against the government's involvement in Daijosai. These cases were ultimately rejected.
Last year, over 300 The complainant, including Christian priest Takuya Hoshide, filed a lawsuit against the government for funding the repression rituals with public money.
"If we allow (state funding of Daijosai) to happen, we help create the society that chokes our ability to say no to the imperial myth," he said. "We need to create a society where we can have some religious faith."
Although Naruhito's father broke with the tradition in a number of ways – including becoming the first monarch to marry a commoner and the first two centuries abdicating the throne – Breen believes that the tradition of Daijosai will likely continue, especially as opposition has diminished.
"It is part of the modern tradition of emperor creation and it seems to be the emperor's desire to implement it. I expect it to be implemented in the distant future," he said.
CNN's Yoko Wakatsuki contributed reporting from Tokyo.