Haruki Uemura, president of the All Japan Judo Federation, said Tuesday he has accepted the resignation of board member Kazuo Yoshimura.
Yoshimura had appointed Ryuji Sonoda as the national women's head coach in 2008. Sonoda, accused of physically abusing 15 top judoka in his charge, resigned last week.
"I thought it would be appropriate to resign as the head of athlete development within the federation," Yoshimura said at a news conference.
The women's team, including 78-kg London Olympian Akari Ogata and 48-kg world champion Haruna Asami, left for Paris on Tuesday for the Judo Grand Slam this weekend.
The athletes were shielded by federation officials at Narita International Airport and did not comment on what sports minister Hakubun Shimomura described earlier in the day as "the most serious crisis in Japan's sports history."
After the team departed, the federation announced the resignation of assistant coach Kazuhiko Tokuno, who returned to Japan, cutting short a trip to Europe.
The federation said Tokuno resigned because he admitted being involved in the abuse.
On Monday evening, a lawyer for the 15 elite female judoka who allege they were abused during Olympic training by Sonoda said the athletes want the federation to overhaul its entire staff, not just one coach.