The Blues' stuttering start to their Premier League title defence has paled in insignificance due to the incident towards the end of Saturday's 2-2 draw with Swansea.
Chelsea boss Mourinho was visibly infuriated to see head physiotherapist Jon Fearn and first-team doctor Carneiro run on to the field to give Eden Hazard treatment.
The Portuguese told the media afterwards that their "impulsive and naive" decision showed they did not "understand the game" and, since then, Press Association Sport has learned Carneiro's role at Chelsea is changing significantly.
While remaining as first-team doctor, she will no longer be involved in matches and training sessions - a situation Fearn is also reported to find himself in.
The move has led to widespread criticism, which Mourinho will face up to for the first time at 12.30pm on Friday as Chelsea have called a press conference to preview the trip to Manchester City.
The Premier League Doctors' Group has expressed its concern over the ongoing situation and says a reduction in Carneiro's role would be "unjust in the extreme".
Peter Brukner, formerly Liverpool's head of sports medicine and sports science, called Mourinho's behaviour "absolutely appalling", while FIFA's chief medical officer Jiri Dvorak has thrown his support behind Carneiro.
"I can't see such a situation and we have to defend the position of the doctor," Dvorak told Sky Sports News.
"Everyone involved has to respect the fact the doctor is in charge.
"I don't want to interfere with the club as such, but I would endorse clearly what the team doctor and the physiotherapist did
When they were asked, they had to come on to the pitch."
Footage released by Sky Sports on Thursday revisited the animated scenes on the touchline from Saturday's match, with Mourinho showing his anger towards Carneiro and Fearn.
Stressing the importance of football club doctors being left to do their job, Dvorak said: "In medical aspects, in medical diagnosis, the manager has nothing to say."
Carneiro joined Chelsea in February 2009, having previously worked at the British Olympic Medical Institute and with England Women's Football and UK Athletics.
The doctor thanked people for their support on Sunday, posting on Facebook: "I would like to thank the general public for their overwhelming support
Really very much appreciated."
The post has attracted 40,000 likes to date and reports suggest Carneiro is seeking legal advice.
Fearn joined Chelsea from Reading in 2010, where he was head of sports medicine for nine years
He has also worked as West Ham's first-team physio.
Source : PA
Source: PA