The Japan Amateur Boxing Federation is facing a wide range of allegations of misconduct, including the inappropriate use of grant money.
More than 300 people with links to the sport made the allegations. They called on the Japan Sports Agency, the Japan Sport Council, and other institutions to open an investigation.
They say grant money intended for one athlete was divided and given to three people at the federation's instruction.
The complaint also alleges that some judgments in official matches were unfair.
During a national sports event in 2016, a boxer from Nara Prefecture who was knocked down twice won the match.
In response, the federation issued a statement on Wednesday.
The federation admitted to the allegation on the grant. It said the chairman, Akira Yamane, asked the intended recipient to share the money with 2 other people.
But the federation vehemently denied the allegation of unfair judgment. It says points are given according to the number of clean hits, not for knockdowns themselves.
But one judge told NHK of his experience in giving a win to a boxer from Nara Prefecture at a close match in consideration for Yamane. Nara is Yamane's home prefecture.
He says he has many times witnessed Yamane using harsh words toward judges when boxers from Nara lost.
The chief of the Sports Agency, Daichi Suzuki, has already expressed his intention to launch an investigation in conjunction with the Sport Council.