Bitter comments and angry reactions sent shock waves through the Olympic movement on Monday.
The discord erupted at a convention for the international federations that govern each sport worldwide.
Marius Vizer, chief of the umbrella SportAccord organization, accused the International Olympic Committee of perpetuating a system that is "expired, outdated, wrong, unfair and not at all transparent.''
The IOC could be "headed for destruction" if it does not change, he said.
Vizer, who also heads the international judo federation, made his opening remarks with IOC President Thomas Bach in attendance at the meeting in Sochi, Russia.
Within hours, the international federations for shooting and track-and-field resigned from SportAccord in protest of the speech. Other federations signed a letter of support for Bach.
Vizer has long believed the IOC interferes with the business of the numerous federations, which set the rules and run competitions in each sport. He also described the creation of an Olympic TV channel as a waste of money.
Bach subsequently fired back in his address to the convention, saying the IOC has maintained a running dialogue with the federations.