The JOC says on Tuesday it cancelled a 250 million yen ($2.6 million) annual subsidy for the federation. The JOC directive also included a ban on violent coaching, more transparency in team selections, and increased hiring of female coaches.
The issue surfaced after 15 female judokas accused former national coaches of harassment and physical violence during training before the London Olympics.
The JOC aims to eliminate similar abuses as Tokyo vies to host the 2020 Games.
Corporal punishment in Japanese sports has come under the spotlight since a Japanese high school student committed suicide in December after repeated beatings by his basketball coach.