Appearing before the Culture, Media and Sport Committee on 16 January, Masters used the term "small clubs" when answering a question about the two.
Everton and Forest have both been charged for alleged breaches of profit and sustainability rules (PSR).
Committee chair Caroline Dinenage said the remark "raises wider questions".
Committee member Damian Green had asked Masters whether big clubs were treated differently to others when it came to the league's PSR.
Both Everton and Forest have been charged - with Everton already appealing against a 10-point deduction for a separate breach of the rules, which are designed to keep club spending sustainable.
Manchester City were charged with more than 100 breaches of financial rules in February 2023 but are yet to face a hearing, with Masters also telling last week's hearing he understood why Everton and Forest fans might be frustrated by that.
In answering Green he said: "The standard directions [on PSR] are for everybody, they're not just for the small clubs."
It led to criticism from fans of both clubs on social media.
"Richard Masters' implication that nine-times league title winners Everton and double European Cup winners Nottingham Forest are 'small clubs' will have raised eyebrows with fans," Dame Dinenage said.
"To suggest clubs are categorised according to size raises wider questions about whether every member of the league truly does receive treatment that is fair and consistent."
In its letter to Masters, the committee also wants him to explain the league's role in sanctioning clubs, saying "his insistence that the charges and punishment regime is entirely independent of the Premier League" was "puzzling".
The committee has also urged Minister for Sport Stuart Andrew to bring forward the Football Governance Bill, which would establish an independent regulator for football, "as soon as possible".
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