The two clubs will be England's representatives in FIFA's expanded 32-team event in the United States, with players' unions threatening legal action on welfare grounds and national leagues unhappy about the potential knock-on effects on their own competitions.
The Club World Cup final is due to be played on July 13, with the 2025/26 Premier League season starting on August 16.
"The leagues and the players' unions are not happy with the decisions that are being taken at a global level," Masters told Sky Sports.
"We've seen the Club World Cup come in, and obviously that is going to have an impact on the Premier League.
"If either Manchester City or Chelsea get to the final of that competition, the Premier League starts four weeks later, and all players are supposed to have three weeks off as part of the contractual commitment.
"So how does that work? With great difficulty I would say."
'Premier League is not a pension fund'
Masters, meanwhile, insisted English football is "not on a financial precipice" as he reiterated the Premier League's concerns about the potential impact of an independent regulator on the game.
The Premier League spent more than £45 million ($56 million) in legal costs during the 2023/24 season as it attempted to uphold its rules amid challenges from clubs.
And there will have been additional and significant legal fees this season for the Premier League given their major disciplinary case against Manchester City is still ongoing.
The reigning champions were charged in 2023 with more than 100 alleged breaches of the Premier League's financial rules.
An independent commission heard the case between September and December, with an outcome now pending.
City have also challenged the legality of the league's associated party transaction (APT) regulations, which seek to ensure deals done with organisations linked to a club's ownership are at a fair market value.
Both the current and former British government's aim in supporting an independent regulator is to safeguard the financial sustainability of clubs in the top five tiers of English football.
Masters, however, insisted too many regulations could damage the excitement on which the Premier League thrives.
"We have that jeopardy, we have that constant fizz of compelling entertainment," he said.
"There are many different reasons (for the Premier League's global popularity) but that, I think, is what separates us from others."
He added: "We have always been pro investment within measured risks. The Premier League is not a pension fund, it is a place where capital is put at risk. There is no certainty of outcome -- that is one of the things that makes it interesting.
"We do worry that a new regulatory function might be risk-averse and might inhibit clubs' ability to invest. And the ability to invest is key to competitive balance, and that jeopardy that I'm talking about."
