Shukan Shincho weekly has reported that a representative of Crown Prince Naruhito's household contacted the elite Gakushuin Primary School and recommended that medicine to treat attention deficit hyperactivity disorder was added to meals.
Princess Aiko, 8, was left traumatised by an encounter with a group of misbehaving boys back in March.
The agency says she was only able to attend the first hour of classes between March 8 and 11 after being shocked at the "rough behaviour" of boys in her grade.
She failed to attend the end-of-year graduation ceremony later that month and missed the April 9 welcoming ceremony for new third grade students. Since then, Princess Aiko has attended school for three hours a day, accompanied by her mother.
"The Imperial Household Agency has asked publisher Shinchosha for an apology and a correction to the baseless and malicious allegation in the weekly magazine that the agency has suggested to Princess Aiko's school that it add medication to school meals for unruly boys to calm them down," a spokesman for the agency said.
The official said the prince's household was "very unhappy" with the reports but added that no official reply has been received from the publisher. He added that if no apology is forthcoming then it would consider "an appropriate response."
The magazine stood by the story.
Kota Osone, a journalist for Shukan Shincho, said, "The story is accurate and we have solid sources for the information."
This latest report will increase the pressure on the prince's household, which is still trying to cope with the widely reported health problems of Crown Princess Masako, Princess Aiko's mother. Now 47, she has rarely been seen in public since 2004 and is suffering from what the palace has admitted is an "adjustment disorder," apparently brought on by pressure due to her inability to produce a son to continue the imperial line.