There had been rumours that the England international would be shown the door at Old Trafford after he was dropped to the bench for United's Champions League defeat to Real Madrid on Tuesday.
Rooney was previously linked with a switch to fierce rivals City before signing a new contract at Old Trafford, but Mancini has played down a summer swoop for the frontman.
"I understand that Rooney could be upset that he didn't play [against Real Madrid] but these things can happen in every team," the Italian said in a press conference. "I think that Rooney's one of the best striker's in Europe but I think that it's difficult that he can leave Manchester United."
Rooney currently has two years left on his contract at United.