Aleksander Ceferin, the head of UEFA, boycotted the World Cup final to show unhappiness with FIFA, British media reported on Monday.
The relationship between European football's governing body and the game's global federation is under strain.
One cause was FIFA's unexplained decision to suspend a red card for United States striker Folarin Balogun before a World Cup game against Belgium after US President Donald Trump asked FIFA head Gianni Infantino to "review" the sending off.
UEFA was unhappy that Infantino bowed to perceived political pressure from the host and called the decision by FIFA's disciplinary committee "unprecedented, incomprehensible and unjustifiable" and said it "crossed a red line".
Other sources of tension were FIFA's acquiesence when US authorities refused to allow Somali referee Omar Artan to enter the country.
UEFA responded by appointing Artan to officiate its Super Cup final next month.
FIFA was also unable to ensure Iran was treated the same way as other teams playing in the United States.
Coach Amir Ghalenoei said his team were the "most oppressed" at the World Cup.
US Homeland Security Secretary Markwayne Mullin said he "danced a happy dance" when Iran were knocked out.
UEFA has also, so far, refused to adopt some of FIFA's World Cup innovations, such as hydration breaks, the "mistaken identity" VAR protocol, which led to the sending off of Breel Embolo in Switzerland's quarterfinal loss to Argentina, or the cards for players who cover their mouths talking to an opponent.
Ceferin also criticised the enlarged 48-team tournament before it kicked off.
"We have a lot of matches that are completely uninteresting," he was quoted as saying in a newspaper in his native Slovenia.
Ceferin has also been publicly critical of World Cup ticket prices.
UEFA has said that it would continue to offer two 'fan first' ticket categories at the 2028 Euros in the United Kingdom and Ireland. It said that 40 percent of tickets would either be priced below £30 or below £60. It has also promised not to adopt dynamic pricing.
Ceferin did attend the opening match of the tournament in Mexico City on June 11.