Premier League chief executive Richard Masters says he "did not intend" to suggest Everton and Nottingham Forest were "small clubs".
Masters used the term last month when answering a question at a Culture, Media and Sport Committee hearing.
Both clubs have been charged for alleged breaches of Premier League financial rules.
Committee member Damian Green had asked whether big clubs were treated differently over the matter.
In answering Green, Masters said: "The standard directions [on the Premier League's profit and sustainability rules] are for everybody, they're not just for the small clubs."
His comment was criticised by Forest owner Evangelos Marinakis, while Masters was asked by committee chair Dame Caroline Dinenage to clarify his remarks, with the MP saying they "raised wider questions".
In a written response, Masters explained that in his answer he had "sought to emphasise that the Premier League's rules apply equally to all clubs".
He went on: "Furthermore, I am happy to confirm that, while clubs can be delineated by many different measures, no such criteria or classification is used by the Premier League.
"As I said in my evidence, Everton and Nottingham Forest are valued and respected members of the Premier League.
"Both clubs enjoy successful histories, have strong and passionate fanbases, and make a significant contribution not just to the Premier League's vibrant competition, but also to their cities and local communities.
"By reflecting the committee member's framing of the question, I did not intend to suggest otherwise. It would be incorrect to infer from this that there is any unfair treatment based on club size, as suggested in the committee's media statement.
"Indeed, the point I made was the opposite, in that the Premier League board applies the rules consistently, irrespective of the club in question."
Manchester City were charged with more than 100 breaches of financial rules in February 2023 but are yet to face a hearing
Masters also reiterated that the commission which heard Everton's case, when they were deducted 10 points for a separate breach of the rules, is independent of the Premier League.
The Goodison Park club have appealed against the decision with a verdict due shortly.
"The panel members are appointed by an independent chair in a process in which the League plays no part, and members of each commission are appointed by that chair independently, again in a process in which the League plays no part," he said.
"Each member of the independent commission that heard this case was a senior and experienced lawyer or financial expert, including one former member of the judiciary."
