International judo federation president Vizer, whose SportAccord group represent close to 100 Olympic and non-Olympic federations and organisers of multi-sports games, said IOC president Thomas Bach interfered with the autonomy of sporting bodies.
"The Council met today in Sochi and reviewed the statements and report of the SportAccord leadership to its annual general assembly yesterday and considers the position taken not compatible with the role and mission of ASOIF as a major stakeholder of the Olympic Movement," the ASOIF said on Tuesday.
"ASOIF Council unanimously decided to suspend ASOIF's association with SportAccord with immediate effect pending a full review."
Vizer's comments triggered instant reaction with the world athletics federation (IAAF) immediately withdrawing its SportAccord membership, while the International Paralympic Committee (IPC) followed suit on Tuesday.
Fifteen federations, including soccer's FIFA, also opposed the remarks.
"I always tried to develop a constructive collaboration with the IOC and with president Bach," Vizer said at the opening of SportAccord's convention in Sochi, Russia. "Unfortunately it never became reality.
"Mr President, stop blocking the SportAccord strategy in its mission to identify and organise conventions and multi-sport games. Do not try to create a theory around which sports are and are not eligible for multi-sport games.
"The IOC system is expired, outdated, wrong, unfair and not at all transparent."
The IOC has had an uneasy relationship with Vizer, who took over SportAccord in 2013 and unsuccessfully attempted to set up his own international multi-sports event, the United world Games.
Vizer also rejected the IOC's Agenda 2020, Bach's brainchild and a series of reforms to make the Games more attractive and relevant to fans, bid cities and sponsors.
"My impression is your opinion you have exclusively for you," German Bach said after Vizer's speech before getting the backing of more than a dozen federations, including football, swimming, athletics, sailing, hockey, badminton, shooting and triathlon among others.
"We the undersigned...are expressing our disagreement on the opinions expressed this morning by the SportAccord president ...which do not reflect the views of the international federations," they said in a letter.
The IPC said in a statement that they fully support the IOC and Bach, "a man who through Olympic Agenda 2020 is pushing through the unanimously approved reforms he promised in his election manifesto."
(Reporting by Tony Jimenez; editing by Toby Davis)
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