Women in Football said its language expert is certain Mourinho used abusive language towards a woman, contrary to the verdict of the FA's chosen expert.
"It's another example of the FA failing to tackle discrimination," it said.
"We are concerned by the serious flaws in the process of such investigations."
The FA studied footage from the 2-2 draw with Swansea on 8 August after a member of the public made a complaint.
It said it was "satisfied the words used do not constitute discriminatory language under FA rules".
Carneiro and head physio Jon Fearn were criticised by Mourinho for treating Eden Hazard with the side a man down.
The club doctor, 42, had her role downgraded before she decided to leave the club.
The Women in Football statement said: "Our own language expert made it abundantly clear that the abusive words used by Mr Mourinho on the touchline that day were specifically directed towards a woman, as indicated by the grammar of his sentence.
"Other Portuguese speakers we contacted in gathering evidence also emphasised this point. We therefore find it extraordinary that any expert or Portuguese speaker would report otherwise."
The FA said it had appointed an independent academic expert in Portuguese linguistics to analyse the footage of the incident, which included the audio recording.
It said in its statement: "Both the words used, as translated and analysed by the independent expert, and the video evidence, do not support the conclusion that the words were directed at any person in particular."
The Football Association's decision to clear Chelsea manager Jose Mourinho of making discriminatory comments to former club doctor Eva Carneiro has "appalled" a campaign group.