To avoid Qatar's fierce summer heat, the 2022 World Cup is being moved from its traditional June-July slot, resulting in European competitions stopping for around two months.
Fearing losses of around $70 million if the league shuts down, the Spanish league appealed against FIFA's scheduling change to the Court of Arbitration for Sport.
UEFA General Secretary Gianni Infantino suggested La Liga President Javier Tebas' public protest was because he "wants to get some publicity out of it."
"It's a bit sad that people don't accept decisions taken by a vast majority," Infantino said after a UEFA meeting in Prague. "You cannot take all decisions unanimously because otherwise you would not take any decisions anywhere. You need to be a bit flexible."
Infantino said the "the vast majority of leagues," and the European Club Association accepted playing the World Cup for the first time at the end of the year.
But the ECA and European Professional Football Leagues organization jointly suggested starting the World Cup in May — a proposal rejected by FIFA's executive committee in March. Some of the tensions were calmed when FIFA agreed to pay clubs worldwide $209 million for releasing players for both the 2018 and 2022 World Cups.
"We need to take a little bit of heat out of this whole discussion," Infantino said. "We need to be a bit more realistic, and reasonable, and pragmatic on certain things. We don't need to take ourselves too seriously.
"The World Cup is the best national team competition in the world. It has to be played if at all possible in the best conditions. If this means that for one year in 150 years of history of football, we change the calendar ... it will not be the end of the world."
UEFA President Michel Platini could be in charge of FIFA as it grapples with the lingering fallout of the 2010 decision to vote for Qatar.
But at UEFA's executive committee meeting at a former monastery in Prague, the former France captain stayed silent on whether he will look to succeed Sepp Blatter in the FIFA presidential election, which will be in December or January.
Platini's ambitions should become clearer after FIFA's executive committee sets the election date at an emergency meeting on July 20 in Zurich.
Blatter announced plans to quit this month — four days after being elected for a fifth term — under pressure from FIFA sponsors over the escalating criminal investigations into soccer officials.
"The sooner there is clarity about what will happen with FIFA, the better for FIFA and also for football," Infantino said.
UEFA's executive committee met ahead of the final of the European Under-21 Championship late Tuesday, when Portugal met Sweden.
The meeting decided on the venues for the 2017 UEFA finals. The Champions League showpiece will be at Cardiff's Millennium Stadium, and Stockholm's Friends Arena has the Europa League final. The Super Cup between the winners of the two UEFA club competitions will be in Skopje, Macedonia, at Philip II Arena.
Karel Janicek contributed to this report.
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