Chairman Greg Dyke said the Football Association is still of the view that the leaked Richard Scudamore sexism emails are "totally inappropriate," but no action will be taken.
Mr Dyke reiterated in a statement that the FA had "made it clear that Mr Scudamore was not an employee of the Football Association."
The FA chairman also said that he had been reassured the Premier League's decision to back Mr Scudamore had "followed proper process" and came after a "thorough investigation."
The former personal assistant to Richard Scudamore has written an article in which she calls the Premier League's decision to back their boss a "kick in the teeth for women."
Rani Abraham leaked emails from the Premier League chief executive containing sexist conversations about female colleagues.
Writing in a column for The Guardian, Miss Abraham said she felt "there's been a real injustice, that they're not taking any notice of what he did."
She also raised her fears that "maybe the Premier League's decision will send out another signal entirely and bosses will think: 'If Richard Scudamore can get away with it, so could I'."
The Premier League chief executive has apologised for his remarks.
Treasury minister Andrea Leadsom has said that there is a culture within some key sports which "tolerates sexism".
Responding to criticism of Premier League chief executive Richard Scudamore over leaked emails, she told ITV News: "I haven't looked at apparently some of the more salacious emails, but I do think there is a culture, particularly in some of the key sports, that does perhaps tolerate sexism."
She added: "I think it is incredibly unfortunate, because we can all take a joke, but actually it's very important that women are seen as colleagues and equals and encouraged to the best they can do."
"It depends. When does a joke become something that is actually harmful and humiliating for woman? I can't really comment in this particular case, but personally I would like to see men in particular respecting their colleagues as equals whether they are men or women."
A Football Association equality panel will meet later today to discuss the leaked emails from Premier League chief exec Richard Scudamore.
Yesterday the Premier League investigation said there would be no further action and no further disciplinary action over the emails.
The advisory board, chaired by independent member Heather Rabbatts will look into the emails and the Premier League's handling of the case.
Yesterday David Cameron added his voice to the row, saying he did not think a minister would survive the scandal.
Richard Scudamore has "done a fantastic job" at the Premier League, prior to the scandal caused by leaked sexist emails, former Manchester United footballer Dwight Yorke said.
Speaking before an official statement from the Premier League said Scudamore would face no further action, Yorke said the League Chief Executive had made an "elementary mistake."
Les Ferdinand has said that racism and sexism have no place in football.
Speaking to ITV News after a series of emails containing sexist comments from Premier League Chief Executive Richard Scudamore were leaked, the former England international said;
"We talk about racism, we talk about sexism - and all these things shouldn't be in football."
Ferdinand was speaking before the Premier League ruled that Scudamore wouldn't face any further action for the emails.
An Investigation into the conduct of Premier League Chief Executive Richard Scudamore has found "no climate of disrespect of women in the workplace," an official statement has said.
"Responses from many women in employment at the Premier League, and extensive consultations with others, establish that there is no climate of disrespect of women in the workplace." The statement said.
The Premier League has ruled that "no further disciplinary action is required or justified" for Richard Scudamore after a series of leaked emails revealed sexist slurs.
In a statement to the media, the Chairman of the Premier League said that the Clubs had accepted the Chief Executive's "sincere" apology and "accepted his undertaking to take active steps to prevent a recurrence."
"In these circumstances and in the light of a previously unblemished record over 15 years of service to the Premier League, the Clubs resolved unanimously that no further disciplinary action is required or justified." The statement said.
Prime Minister David Cameron has supported the view of his sports minister that Richard Scudamore's comments were "unacceptable", but said that it was for the Premier League to decide his future.
The Prime Minister's official spokesman said: "Helen Grant...was right to say what she did, I have clearly associated the Prime Minister directly with those remarks.
"But in terms of staffing decisions at the Premier League, it's for the Premier League."