"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," Carneiro said in a statement.
The FA had failed to interview her to establish if she was the victim of alleged sexist abuse by the Chelsea manager, she said.
The FA said this week it was not taking any action against Mourinho following the incident at the opening Premier League game of the season against Swansea City on August 8.
Mourinho's behaviour has been criticised by the FA's own chairman Greg Dyke who said on Thursday that Mourinho should have apologised, while Heather Rabbatts, an FA independent board member, was also highly critical of the way the FA conducted itself.
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Carneiro said that the FA had "chosen to ignore" some of the evidence, adding that they also failed to act when she was the subject of sexist abuse from West Ham United supporters last season.
"I was surprised to learn that the FA was allegedly investigating the incident of August 8 via the press," Carneiro said. "I was at no stage requested by the FA to make a statement."
She added: "Choosing to ignore some of the evidence will surely influence the outcome of the findings."
Mourinho refused to comment on the case when he spoke to reporters at his weekly media briefing on Friday ahead of Chelsea's Premier League match with Southampton on Saturday.
Mourinho accused Carneiro and Jon Fearn, the Chelsea physiotherapist, of being "impulsive and naive" and failing to "understand the game" when they entered the field to treat Eden Hazard late in a match against Swansea.
Chelsea were already down to 10 men following the sending-off of goalkeeper Thibaut Courtois and Mourinho lost his temper when the pair went to treat Hazard, meaning the team were temporarily reduced to nine men.
The FA cleared the Chelsea manager of making discriminatory comments to Carneiro but Dyke said in a letter to FA Council members that the Portuguese had been in the wrong.
"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," Dyke said.
"Instead he has said very little and Miss Carneiro has lost her job.
(Editing by Clare Fallon)
