Russian Deputy Prime Minister Vitaly Mutko, who is also head of the Russian Football Union (RFU), says he has been barred from running for reelection for a place on the FIFA Council.
Mutko said he would not appeal the decision.
His statement came hours after FIFA sources told media outlets that Mutko had failed an eligibility test carried out by the world soccer body's review committee.
Mutko told Russian state news agency TASS that new "political neutrality" criteria barred him from vying for the post, but added that the decision would not affect Russia's preparations to host the 2018 World Cup.
Mutko has held a seat at FIFA's top table since 2009.
He was promoted to the position of deputy prime minister in October after having served as sports minister since 2008.
Mutko has also been accused of involvement in what the World Anti-Doping Agency (WADA) said was a large-scale state-orchestrated doping scheme in Russian sports.
Russian track-and-field athletes and Paralympians were barred from the Rio Olympics last summer because of the doping scandal.
However, FIFA sources told media outlets that Mutko had been barred because of his current political position, saying that the decision was not linked to the doping scandal.