A source close to FIFA in Zurich said football's governing body has barred Mutko from taking up a seat on the organisation.
Damning reports of state-sponsored doping and allegations of graft over Russia's hosting of the 2018 World Cup and the 2014 Sochi Winter Games have done little to undermine his reign as the country's sports tsar.
On Friday, a source close to FIFA in Zurich said football's governing body has barred Mutko from taking up a seat on the organisation.
The source said the decision was taken because of potential conflicts of interest with Mutko's government role, and denied there was any link to accusations of involvement in doping.
Mutko, the former sports minister, was promoted to deputy prime minister in October, two months after he and many Russian athletes were barred from the Rio Olympics for what the World Anti-Doping Agency called "state-dictated" doping.
The 58-year-old Mutko, known for contradictory statements and diatribes against critics of Russian sport, has insisted that Russia will reform its scandal-ridden anti-doping system but has denied state complicity in doping cover-ups.
But WADA has said it was "not possible" that Mutko was unaware of the widespread rot in Russia's anti-doping system.
At a time when relations between Russia and the West have sunk to a post-Cold War low, Mutko has suggested that Russian sport is a victim of a new Cold War.
He has repeatedly rebuked the West for what he says are attempts to sideline Russia from international competition.
"Not one athlete in the world is being suspended for what Russian athletes are being suspended for," Mutko told R-Sport news agency in January.
Last month Mutko also lashed out at Russian athletics coaches. He said that they "don't understand how to work without doping" and that dozens of them had been fired.
The Kremlin has vowed to suspend officials implicated in a WADA probe by Canadian lawyer Richard McLaren but insists Mutko had done nothing wrong.
Mutko's former deputy Yury Nagornykh, reportedly the sports ministry's pointman for covering up positive doping tests, resigned after being suspended over the report, while Mutko's former adviser Natalia Zhelanova also lost her job.
A programme by German public broadcaster ARD last year suggested that Mutko had been involved in the covering up of positive doping tests of a footballer from FC Krasnodar in 2014, a claim he dismissed as a "deliberate attack" on Russia.
Mutko has fended off major scandals such as WADA's findings on Russian doping and more trivial ones such as revelations that he expensed nearly 100 breakfasts during a lavish 20-day trip to the 2010 Olympics in Vancouver.
Former colleagues say his ability to shrug off scandal has helped Mutko remain at the top of Russian sport.
"He distinguished himself by the fact that we would extinguish scandals," said Andrei Malosolov, the former head of the Russian Football Union's press service, who worked with Mutko.
Mutko, who also heads the Russian Football Union and was president of Zenit Saint Petersburg from 1997 to 2003, has also overseen a push by Russia to increase its presence in international sports governing bodies.
Meanwhile Russia's Paralympians and the vast majority of its track and field athletes remain barred from international competition. The country has been stripped of several events, including the 2017 bobsleigh and skeleton world championship.
Mutko's tenure has come as the judo-loving Putin has spent considerable resources on sport to bolster Russia's international image.
The country spent exorbitant sums on hosting the Sochi Olympics and to win the right to stage the World Cup in 11 cities next summer.
As with many high-ranking officials, Mutko's ties to Putin date to the early 1990s, when they both worked in the mayor's office in Putin's hometown of Saint Petersburg.
"They had friendly relations," Lyudmila Fomichyova, who worked in the same office, told AFP. "Putin does not give up on his people."
Sociologist Olga Kryshtanovskaya, who studies the Russian elites, says that Mutko has maintained the Kremlin strongman's trust because of his unwavering loyalty.
"Putin gives orders and these orders are fulfilled," she said.
"Putin considers that Mutko does this, which is why he is apparently considered effective."