The emperor, 59, officially began his reign in May after the abdication of his father, the then-Emperor Akihito.
But, after a series of traditional rituals inside the imperial palace in Tokyo, his ascension has now been formalised.
As about 2,000 people looked on, the curtains of the Imperial Throne called ‘Takamikura’ were opened, revealing Emperor Naruhito dressed in a traditional robe.
The ceremony comes as Japan reels from the effects of Typhoon Hagibis, which left almost 80 people dead.
A celebration parade was postponed out of respect for the victims and their families.