Mourinho is ruling out the prospect of Rooney ever being sold to Stamford Bridge after claiming United have vowed they will not do business with Premier League rivals.
Mourinho attempted to lure Rooney to Stamford Bridge last summer and it has already been suggested he will return with another offer if United fail to qualify for next season's Champions League.
United are keen to open negotiations with the 28-year-old, whose present deal expires in 2015.
Yet Mourinho suspects Rooney could be heading abroad if United cannot persuade him to commit to new terms.
Speaking ahead of Sunday's Premier League match between his team and United, Mourinho told national newspapers: "Man United made it clear in the summer they don't swap or sell players to their direct rivals.
"They were clear in the way they approached the Rooney situation. For them, it's pretty clear. They don't swap. They don't sell.
"I think maybe this summer they will try to sell to a non-direct rival. But they were very clear."
The Chelsea manager's comments were put to Moyes, who said: "I can only tell you that I disagree - although he will go to Brazil!"
The Scot passed up an invitation to criticise Mourinho over the timing of his comments - barely 24 hours before the teams meet on Super Sunday.
He said: "Everybody has their style. I wouldn't talk about other managers at other clubs and I wouldn't talk about other players at other clubs.
"I can't tell you what his motivation is but only time will give you an answer about Wayne. The club will deal with that - they will do all they need to do, no question."
Moyes also refused to resort to similar tactics regarding Mourinho's players, including the unsettled Juan Mata.
"I don't talk about players at other clubs. It's not my style," the Scot said.
Rooney is approaching the 10th anniversary of his move to United. He joined from Everton in August 2004 and is the fourth highest goalscorer in United's history.
A groin injury means he will be absent from the line-up for Sunday's match at Stamford Bridge.