Carneiro 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.
In a statement to Press Association Sport she 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."
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.
Mourinho was cleared by the FA of making discriminatory remarks but independent board member Heather Rabbatts criticised the FA for not interviewing Carneiro herself
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."
She also thanked Rabbatts for speaking up for her.
"I admire what Heather Rabbatts has done and thank her and friends and colleagues who have supported me at this very difficult time," she said
The FA's position is that its regulatory team asked Carneiro's lawyers if she wished to provide any evidence
However she says no request was made to speak to her - and she was still formally employed by Chelsea at the time
Rabbatts, head of the FA's inclusion advisory board, said she had "major concerns" regarding the FA's disciplinary process which saw Mourinho cleared, and that the FA's handling of the case was "seriously disappointing"
FA chairman Greg Dyke did criticise Mourinho's handling of the incident however
I n a letter to FA council members, a copy of which has been obtained by Press Association Sport, he said Mourinho committed "a failure of his personal judgement and public behaviour"
Dyke says in the letter: "Personally I don't think Mr Mourinho comes well out of the whole saga - he clearly made a mistake in the heat of a game, and should have said so and apologised
"Instead he has said very little and Miss Carneiro has lost her job.
"Our regulatory team have investigated this and whilst Mr Mourinho has breached no rules it was clearly a failure of his personal judgement and public behaviour
This should be seen as such by the game."
Source : PA