Everton said in a statement the club was disappointed by the decision.
"The club strongly contests the allegation of non-compliance and together with its independent team of experts is entirely confident that it remains compliant with all financial rules and regulations," it said.
"Everton is prepared to robustly defend its position to the commission.
"The club has, over several years, provided information to the Premier League in an open and transparent manner and has consciously chosen to act with the utmost good faith at all times."
Everton narrowly avoided relegation from the 20-team league last season, finishing 16th. They are again fighting to stay up this season and are currently 15th, just three points clear of bottom side Southampton.
Under Premier League rules, teams can make a maximum loss of 105 million pounds over three years, although special allowances were made for the COVID-19 pandemic.
Everton have recorded a total loss of nearly 372 million pounds in the past three seasons.
The club, owned by Farhad Moshiri, has attributed at least 170 million pounds of that to the impact of the pandemic.
Financial fair play regulations are designed to stop clubs running up big losses through spending on players, as well as ensuring sponsorship deals are genuine commercial agreements.
Champions Manchester City were referred last month over more than 100 alleged breaches of finance rules since the club were acquired by the Abu Dhabi-based City Football Group.
Clubs found to have breached the rules risk points deductions, fines or reprimands.
Everton have played every season since 1954-55 in the top flight.