Tensions have bubbled between club and country after the in-form defender was forced to return from international duty through injury.
Jones reported for England with a thigh problem that had been managed for a number of weeks, only to be forced off midway through the first half of the goalless draw with Germany.
The 25-year-old felt discomfort in his left thigh, ruling him out of Saturday’s win against Newcastle as Mourinho claimed the centre-back had six injections to play the friendly.
The United boss again took aim at the FA after ruling Jones out of tonight’s Champions League match at Basel and this weekend’s return to Premier League action at home to Brighton.
Asked if he had spoken to England manager Gareth Southgate and if he wanted to, Mourinho said: “No.
“I think it’s a conversation between doctors because I’m not a doctor.
“I just get information from my doctor, and the information from my doctor was that they consult him in relation to Phil Jones with a little problem in the knee when the national team starts working.
“But then no more contact. The local injections before the match, we were not informed (about).
“Apart from that, I don’t have to speak with Southgate. I just wish (him) good and want him to be successful.”
While his frustrations were clear, Mourinho spoke of his belief that England have “all the conditions” to challenge at next summer’s World Cup.
However, the United boss jokingly spoke of his hope that recently-overlooked Chris Smalling would not be there given his players’ injury problems on England duty — a chance to make a thinly-veiled dig at some Premier League clubs.
“I hope he doesn’t get his spot because somebody comes injured, he comes injured,” he said.
“Jones comes injured and (with) real injuries because there are other injuries where the players cannot play in the national team on the Wednesday and are perfect for the Saturday.
“Our injuries in the national team are real injuries. Jones does not play tomorrow and I can say in advance he doesn’t play the weekend too, so you can say that it is a proper injury.”
Jones will miss Saturday’s match against Brighton but Mourinho expects fellow defender Eric Bailly to return after also missing the trip to Basel.
Antonio Valencia, Ashley Young and Juan Mata were not seen boarding the flight to Switzerland, but Marcos Rojo was and is hoping to make his first appearance since sustaining serious knee ligament damage in April.
Zlatan Ibrahimovic also sustained a serious knee injury that night and returned from the bench in Saturday’s 4-1 defeat of Newcastle.
Mourinho again intends to play the 36-year-old off the bench against Basel — a match where a point will confirm their place as Group A winners.
United’s progress would be confirmed before kick-off if CSKA Moscow do not win at home to bottom-placed Benfica in the early match.
Smalling, meanwhile, says he was “surprised” to be dropped by England and have his ability publicly questioned by Gareth Southgate — but the defender does not believe he has anything to prove.
The defender has impressed for United this season, but Southgate overlooked him for the back-to-back glamour friendlies at home to Germany and Brazil as England are moving towards a style of “using the ball from the back and building up in a certain way”.
Those comments compounded Smalling’s omission and clearly grated on the centre-back.
“Was I surprised? Yes, I was,” he said.
“But you don’t play for one of the biggest clubs in the world for as long as I have and probably won the most trophies bar the Champions League without being able to do everything a top defender needs to do, be it playing or defending.”