The 59th head of state officially began his reign in may, but his ascension will only be formalized after he completes a series of rituals.
Its ascent comes as Japan is still reeling from the effects of Typhoon Hagibis, which has left nearly 80 dead.
The parade was postponed out of respect for the victims and their families.
More than half a million people convicted of minor crimes will also be pardoned to mark the enthronement.
The Sokui no Rei – or the Ceremony of Accession – is set to begin at 13:00 (04:00 GMT) on Tuesday.
Emperor Naruhito will ascend the 6.5-meter throne of Takamikura, wearing a yellow-orange tonal robe that only emperors wear on special occasions, according to the Kyodo news website.
His wife, Empress Masako, will sit on a nearby throne.
The ceremony will take place in the presence of an ancient sword and jewel-sacred treasures that act as a symbol of Imperial power.
The 30-minute ceremony will end with a speech by the Emperor, followed by a congratulatory address by Prime Minister Shinzo Abe.
It will be attended by dignitaries from more than 170 countries, including Britain’s Prince Charles.
The Emperor will later hold a tea party for foreign royalties, while Mr Abe will hold a Banquet in the evening.
The enthronement parade, which sees the Emperor travel in an open top car to “meet” the public, has been postponed until November 10.
Pretty huge deal. The last enthronement ceremony took place in 1990, when then-Emperor Akihito officially ascended the throne.
Former Emperor Akihito, Naruhito’s father, abdicated in April this year, becoming the first monarch to do so in more than 200 years.
He received special legal permission to resign, saying he felt unable to perform his role due to failing health.
The role of the Emperor is largely ceremonial, focusing on interactions with citizens and meetings with foreign dignitaries.
Emperor Naruhito officially began his reign on may 1.
According to the Japan Times news website, the ceremonies held on the day were “simpler and designed to immediately signify the succession to the throne.”
Sokui no Rei will be a much more complicated affair.
It is not uncommon for there to be a gap between the first succession to the throne and Sokui no Rei.
For then-Emperor Akihito, there was a nearly two-year gap between his throne and Sokui no Rei.
According to one Japanese expert, the reason for the confusion this time is that the abdication of the then Emperor Akihito broke away from the usual procedure.
As a rule, renunciations only occur when the king has passed away. The festive enthronement can take place only after a year of mourning.
“Usually the way it happens is that the Emperor dies and then of course they immediately install the next Emperor, but in this case it seems much more normal that the main ceremony (ascension) will take place afterwards because the country is still in mourning ,” said Ken Ruoff, author of the Japanese Imperial house in the postwar era.
But since then-Emperor Akihito retired, Emperor Naruhito’s ascension was seen as much more of a celebration.
“The world just assumed it was a joint celebration, but the real celebration is what’s happening now,” Ruoff told the BBC.
“This is what international representatives come to, and incredibly complex banquets will be held. There was also to be a parade. It’s not perceived as a big deal (for) the rest of the world who are like, ” haven’t we already done this? But it’s a big deal for the Japanese .”
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