Local media reports said Ikki Kodukai, a 24-year-old Tokyo graduate student, may have been acting out of revenge over his wife's romantic involvement with the 42-year-old victim.
Police said Mr Kodukai, who was arrested shortly after the alleged attack, punched the unnamed lawyer several times before prying off his pants and then severing his "lower body part" with the shears.
A Tokyo police spokesman confirmed the body part in question was the man's genitals.
Kodukai told police that he "flushed what was severed down the toilet", he said, adding that the victim's injuries were not life threatening.