The knives were discovered Friday in a classroom at the prestigious Ochanomizu University, where Prince Hisahito attended.
The mysterious discovery comes to the throne just days before Hisahito's uncle, Crown Prince Naurhito. After the abdication of Emperor Akihito this Tuesday.
Hisahito, third in the throne, was reported to be in second place after his father's rise, in another part of the school building, when the knives were discovered.
The name of the resident is noted on every desk so that the prince's desk is easily recognizable, the newspaper said.
School safety recordings seemed to show a middle-aged man wearing a construction worker's uniform and helmet on the school grounds when the knives were discovered.
The school turned to the incident with a statement on their website and promised to review the security protocol.
"We apologize for the great concern we have expressed regarding the incident at Ochanomizu University Junior High School," said the statement attributed to University President Kimiko Murofushi.
"Ochanomizu University will urgently review security measures in consultation with middle school and ensure that these kinds of incidents never happen again."
Hisahito may have a police sting but reportedly can not accompany him to class.
Emperor Akihito resigns the Chrysanthemum Throne – the first abdication of the Japanese throne for 200 years – on Tuesday.
Hisahito's uncle, Crown Prince Naruhito, becomes the country's 126th emperor when he is crowned in a ceremony on Wednesday.
The 12-year-old is the only male grandson of Emperor Akihito and Empress Michiko. Given the inheritance laws that apply only to men, he will come second after his father became crown prince and successor this week as Naruhito ascends.
In August 2016, Akihito made a rare televised speech in which he said that his age and fitness status could make "fulfilling" his tasks "difficult." A request that encouraged many to step aside.
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