Chelsea have made two bids for the England international and have not ruled out making a third, with Rooney reportedly upset by comments Moyes made in pre-season that he would have to play second-fiddle to Dutch striker Robin van Persie.
"They are against me?" Mourinho was reported as saying by The Guardian newspaper on Monday, when asked whether he would get an angry reaction from the United crowd.
"But I didn't say (to Rooney) you will be a second-choice for me. And they are against me?
"We are trying to get a player that a manager told 'You will be a second option' for him. We are not going for Van Persie.
"They don't have to be against me. If I say Ramires is a second option for me and he plays when (Frank) Lampard is tired or injured, if someone comes here to get Ramires, nobody is upset."
He was then asked if Moyes should take the blame, to which he replied: "Of course."
Mourinho later softened his stance, saying that every team had good players that were second-choice.
"The point is if the players are happy to accept that situation," he added.
Mourinho has spoken openly about his desire to bring Rooney to Stamford Bridge and add him to a strike-force that includes Fernando Torres, Romelu Lukaku and Demba Ba.
(Reporting by Josh Reich; Editing by John O'Brien)
