The federation's confirmation Wednesday of Sonoda's actions comes a day after it was revealed 15 female judo wrestlers sent a letter to the Japanese Olympic Committee at the end of 2012 complaining they had been subjected to harassment and physical violence by Sonoda at a pre-Olympic training camp, Kyodo news agency reported.
"If that is true, it would be most deplorable," Japan's sports minister Hakubun Shimomura said. "I have instructed the Japanese Olympic Committee to investigate the matter."
The allegations are the latest in a series of embarrassing incidents for Japanese judo. Last year, two-time Olympic judo champion Masato Uchishiba was accused of raping a teenager.
Japan failed to win a gold medal in men's judo at the London Olympics. The only gold for the nation that invented the sport was won by Kaori Matsumoto in the women's 57-kilogram division.
The use of corporal punishment in Japanese sports has under the spotlight following the suicide in December of a Japanese high school student who endured repeated beatings by his basketball coach.