The man, who has not been named, entered the usually heavily guarded Akasaka residential complex for imperial family members through the adjacent guesthouse on Saturday night, Fuji News Network (FNN) said.
He was caught by the Imperial Guard near the residence of Princess Yuriko, the great-aunt of Emperor Naruhito, about two hours after he broke in, the broadcaster said, quoting police officials.
FNN said the man had gained access via the entrance gate of the guesthouse, which was not guarded at the time.
The break-in was also reported by TBS news, which said the suspect had told police: “I wanted to meet members of the imperial family.”
There were no details on whether the man had encountered any royals, but local media said no one was injured in the incident.
Local police declined to comment and the Imperial Household Agency did not immediately respond to requests for comment.
Naruhito ascended the Chrysanthemum Throne in 2019, after his father abdicated.
He and his wife Empress Masako delivered the traditional New Year’s greeting on Friday by video message for the first time, after their usual appearance was cancelled to avoid crowds gathering as the country battles a third wave of coronavirus.
And in years past, both Japanese and foreigners have been held after swimming across the moat, including a Brit who did so naked.
© Agence France-Presse