The Portuguese doctor was given the opportunity to contribute to the investigation via her lawyers into sexist abuse, according to the FA, denying her claims to the contrary.
The Football Association has rejected former Chelsea doctor Eva Carneiro's criticism of their disciplinary process.
On Wednesday, the FA announced it would take no action against Blues manager Jose Mourinho over allegations of sexist abuse relating to a touchline row with Carneiro during the 2-2 Premier League draw against Swansea City on August 8.
Carneiro, who was removed from matchday duties by the club in the aftermath of the incident and subsequently parted company with the club, questioned the FA's investigation in a statement released earlier on Friday.