Scudamore, 54, was forced to apologise after the comments, made in a private email, were leaked to a Sunday newspaper by the female employee who had a temporary job at the Premier League.
The Premier League announced yesterday that Scudamore would keep his job after acting on the findings of an inclusion advisory board that said there was no discrimination in its working environment.
Scudamore had faced heavy criticism, including from Sports Minister Helen Grant, who called the comments "completely unacceptable".
In a statement FA chairman Greg Dyke reiterated that as Scudamore was not an employee, the organisation could not take a position in terms of employment policy or take disciplinary action.
"We were of the view that was a matter for the Premier League and we asked them to keep us informed of the actions they were taking," he said.
"In terms of wider FA disciplinary action, it was advised that The FA does not as a matter of policy consider private communications sent with a legitimate expectation of privacy to amount to professional misconduct. The FA has applied this policy on an ongoing basis and in relation to numerous other cases."
Peter McCormick, the acting chairman of the Premier League, explained to Dyke how the investigation into Scudamore's comments was carried out.
"He assured me they had followed proper process under their own employment and disciplinary rules and had conducted a thorough investigation.
"We said last week that we considered the contents of the emails in question to be totally inappropriate and are still of that view, as is the Premier League.
"It is important to reiterate the significant focus The FA gives to equality, not least through the work of its Inclusion Advisory Board, and to tackling all forms of discrimination."
The statement added that FA board member Heather Rabbatts, who accused the Premier League of having a "closed culture of sexism" and said Scudamore should give "serious consideration" to his position, would follow up with the Premier League on how the organisations can work together on its inclusion agenda.
Scudamore has helped make the Premier League the most lucrative league in the world since taking over as chief executive in 1999. The competition now has a global TV rights deal worth more than three billion pounds.
(Reporting by Josh Reich; editing by Toby Davis)
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