The Japanese Olympic Committee said in a statement that it had issued 13 directives to the All Japan Judo Federation after the probe carried out by executive board members and a third-party lawyer.
Fifteen current and former members of the women's team had sent a joint letter of complaint to the Olympic Committee alleging harassment and violence by head coach Ryuji Sonoda and his staff in the build-up to last year's London Games.
The athletes said they had been slapped, shoved and beaten with bamboo.
Sonoda announced his resignation in January after the country's sports minister called for a fresh inquiry into the allegations.
"After a thorough review, the committee concluded that serious misconduct had occurred," the JOC statement said.
"The directives include prohibition of violence or misconduct directed at athletes by coaches, the establishment of a framework for athletes to communicate concerns to the organisation's decision makers, clear and transparent procedures for selection of national team members, and the increased hiring of women as coaches and AJJF executives.
"The Executive Board also decided to cut the AJJF's annual subsidy for team development in the fiscal year starting next month," it added.
The JOC said it had set up a system for the anonymous reporting of any violence, harassment or misconduct in sports administered by Japan's national federations.
Japan is the birthplace of the martial art but the team suffered one of their worst judo medal hauls in London with only one gold after being tipped to take home at least seven.
With Tokyo shortlisted against Istanbul and Madrid to host the 2020 Olympics, the Japanese bid team are keen to avoid any negative publicity ahead of September's vote in Argentina.
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