But not everyone is on board the ritual, which was criticized for violating the constitutional separation of religion and state.
The preparations for the ritual began months ago when the shell of a turtle was baked until it broke. The cracks in the shell were then fortune-tended to determine which rice should be grown for the Daijosai, according to the Japaneseologist John Breen, who wrote about the ceremony. In this case, the rice was planted on fields in the prefectures of Kyoto and Tochigi.
During the ceremony Naruhito will offer the sun goddess the freshly harvested rice in two dedicated wooden halls on the grounds of the Imperial Palace. The halls, whose construction cost millions of dollars, are burned down after the ceremony, Breen said.
"The Daijosai transforms the emperor from a simple man to a sovereign, whose authority extends over both empire and the other empire," said Breen. "The Daijosai occurs only once in a reign ̵
Around 700 people – including Prime Minister Shinzo Abe – – have been invited to the ceremony, though they will not go to the halls with the Emperor.
Japan claims it is the world's oldest ongoing monarchy with a tradition of over 2000 years.
What happens during the ceremony?
The emperor will spend about six hours with the sun goddess in two different halls. There are several theories about what happens during the ceremony, involving only the emperor, two "virgins" and the sun goddess, Breen said.
In the 1920s, the state believed that the emperor had done marital relationships with the sun goddess, Breen said. Both rooms are equipped with a bed covered with a silk scarf – and the theory was that the emperor was lying on the bed, covering himself with a cloth and waiting for the sun goddess to come down from heaven and enter his body.
] But this idea has fallen into disfavor. In 1990, when the former emperor underwent the rite, the imperial household rejected the theory on the grounds that the emperor was not lying on one of the two beds. Instead, the beds should "greet the tired sun goddess coming down from heaven," Breen said.
"Yet there is a vital connection between the Emperor and the Sun Goddess, and this is the heart of this Daijosai," he said.
The ceremony dates back to the 7th century, when it was founded to confirm the idea that the Emperor had obtained his right to rule from the Sun Goddess. "If the emperor claims to descend from the sun goddess, the stability of his government is even more certain," said Breen.
Until the 20th century, Japanese rulers were considered the living embodiment of the gods. Naruhito's grandfather, Emperor Hirohito, was the last divine emperor.
After the Second World War, the United States occupied Japan. The country introduced a new constitution prohibiting the imperial family from engaging in political activities, and Emperor Hirohito gave up his divine status.
Today Naruhito is more a symbol of the state than the head of state, and the Japanese emperor exercises no political power.
What is the problem with the ceremony?
The imperial household says that tradition is an integral part of an enthronement – but critics say it jeopardizes the separation of religion and state in Japan.
According to Japan's constitution, the state must refrain from religious activities and can not finance religious institutions. Critics say Daijosai is an example of how the state finances a religious rite – and it goes back to a time when the emperor was considered the human embodiment of a god.
When Naruhito's father, Emperor Akihito, passed the rite in 1990, several civic groups sued the government's involvement in Daijosai. These cases were eventually dismissed.
Last year, more than 300 plaintiffs, including Christian priest Takuya Hoshide, filed a lawsuit against the government for financing the enthronement rituals with public funds.
"If we allow this (government funding of the Daijosai), we are helping to create a society that stifles our ability to say no to the imperial myth," he said. "We have to create a society in which we can have any religious belief."
Although Naruhito's father broke with tradition in many ways – including the fact that he was the first monarch to marry a citizen, and the first in two centuries to abdicate the throne – Breen believes that the tradition of Daijosai probably continues as the opposition has shrunk.
"It is part of the modern tradition of imperial manufacturing and it seems the Emperors wish to do so, and I expect this to happen in the distant future," he said.
Yoko Wakatsuki of CNN reported from Tokyo.