Carneiro broke her silence to insist the FA had never requested she make a statement and effectively ignored some evidence in its investigation into alleged remarks made to her by Mourinho
She also said the FA did not ask her for a statement after being the victim of sexist abuse at West Ham last season and criticised the lack of support from the football authorities.
Carneiro was dropped from first-team duties after Chelsea manager Mourinho criticised her for going onto the pitch to treat Eden Hazard during the opening match of the season against Swansea
She has since parted company with the club, while this week Mourinho was cleared by the FA of making discriminatory remarks.
In a statement to Press Association Sport, Carneiro said: "I was surprised to learn that the FA was allegedly investigating the incident of 8th of August via the press
I was at no stage requested by the FA to make a statement.
"I wonder whether this might be the only formal investigation in this country where the evidence of the individuals involved in the incident was not considered relevant
Choosing to ignore some of the evidence will surely influence the outcome of the findings."
The FA said it had contacted Carneiro's lawyers, who had an opportunity to make a statement
It is understood that had a formal request been made she would have done so but she was still formally employed by Chelsea at the time.
Carneiro's statement added: "Last season I had a similar experience at a game at West Ham FC, where I was subject to verbal abuse
Following complaints by the public, the FA produced a communication to the press saying there had been no sexist chanting during this game
At no time was I approached for a statement despite the fact that vile, unacceptable, sexually explicit abuse was clearly heard.
"It is incidents such as these and the lack of support from the football authorities that make it so difficult for women in the game."
The FA's independent board member Heather Rabbatts has criticised the organisation for not interviewing Carneiro herself.
Mourinho was asked about the Carneiro case three times at his weekly press conference but refused to comment on the controversy
The FA said in response to Carneiro's statement: "We have never received any information or complaint from Dr Carneiro
"Including in written correspondence with her lawyers, it has been made explicitly clear that if Dr Carneiro had evidence to provide or wished to make a complaint she was more than welcome to do so
That route remains open."
Source : PA