The unidentified man, who police said is 36 years old and unemployed, admitted to tearing pages out of 23 books but did not explain his motive. Japanese media, however, questioned his mental competence.
The suspect had been earlier arrested for putting posters at bookstores where Anne Frank diaries were damaged.
More than 300 copies of Anne Frank's diaries were found vandalized in 38 public libraries and bookstores across Tokyo in February.
Police are looking into whether the suspect was involved in all of the incidents.