Chief executive Richard Scudamore insists the Premier League bears no responsibility for the departure of Football Association boss Ian Watmore.
Watmore stepped down as chief executive on Monday after less than a year in the job after growing frustrated his proposals for change were being blocked. He opposed the slow-moving committee structure of the FA and failed to come to an agreement with Premier League chairman Sir Dave Richards on a number of issues.
"What you have to believe is that there is some structural difficulty with it but I think Ian actually had the best chance because of the way he had come into it, the way he had gone about things, his personality," Scudamore told BBC Sport.
"We thought he had the best chance of being able to reconcile what is an association of interests.
"There has been much in the press about vested interests and that is exactly what the FA is, an aggregation of vested interests, whether it be the national game or the professional game and it's how you reconcile those interests that is the challenge.
"But it's not impossible and you can't take away those interests because then what are you left with?"
Speaking about criticism of the Premier League, Scudamore added: "I accept none of it. It's an absolutely impossible thing to level at our organisation, and particularly Dave (Richards). That is just not the sense of it.
"Why I say we are disappointed is that we genuinely felt we were getting somewhere and forget personalities, just organisationally the agenda we were working towards together was the right agenda, the progressive agenda.
"Ian had talked about a regulatory review. He was right in the middle of that and we were absolutely supportive of that review.
"On the other side of stuff - UEFA licensing, financial fair play - we were absolutely as one. So it is very difficult to see and disappointing because the thing we crave most at the FA is stability. Whether people think we do a good job or not, the one thing the Premier League and the Football League have had [in recent years] is stability."