The two clubs will represent England in FIFA's expanded 32-team tournament taking place in the United States.
Players' unions are considering legal action based on welfare issues, while national leagues are expressing dissatisfaction regarding the potential repercussions for their own competitions.
The final of the Club World Cup is scheduled for July 13, just a month before the 2025/26 Premier League season kicks off 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 emphasized that English football is "not on a financial precipice," reiterating the Premier League's apprehensions regarding the potential effects of an independent regulator on the sport.
During the 2023/24 season, the Premier League incurred over £45 million ($56 million) in legal expenses while striving to maintain its regulations in the face of challenges from various clubs.
Additionally, the league is expected to face further substantial legal costs this season due to the ongoing major disciplinary case against Manchester City.
The reigning champions were charged in 2023 with over 100 alleged violations of the Premier League's financial regulations.
An independent commission reviewed the case from September to December, with a decision still awaited.
Manchester City has also contested the legality of the league's associated party transaction (APT) regulations, which are designed to ensure that transactions with entities linked to a club's ownership are conducted at fair market value.
Both the current and previous British governments support the establishment of an independent regulator to protect the financial stability of clubs across the top five tiers of English football.
However, Masters cautioned that an excess of regulations could undermine the excitement that is fundamental to the Premier League's appeal.
“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.”