Mourinho made a concerted effort 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.
However, with Rooney assessing his own options and waiting to see if United can make the necessary signings that would allow them to challenge for major honours, it is thought unlikely the forward will commit himself, leading Mourinho to suggest he could move to a team on the continent next season.
Moyes does not feel the Chelsea manager is correct in his assessment, but he 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," Moyes told reporters.
"Only time will tell and give you the answer (about Rooney). I completely disagree. I can only tell you I disagree.
"The club do the right things, there is no doubt about that. We'll make sure we do the things we need to do."
Moyes also revealed he had received an apology from Chelsea's media department over stories that appeared earlier this week in which Mourinho indicated he had been made aware by someone within the United camp that all was not well at Old Trafford.
Speaking in the Evening Standard, Mourinho had said: "My feeling, which is based on years of communicating with Sir Alex and some inside information, is Man United are not happy."
"I've seen it and had an apology from him and his department," said Moyes, who also was unhappy with the manner his words were reported.
"I think it was poor journalism actually."
Meanwhile, Moyes has insisted there is no issue with England winger Wilfried Zaha, even though Sir Alex Ferguson's final signing as United boss has been so sparingly used this season.
The 21-year-old has made just two substitute appearances in the Barclays Premier League despite United's poor form and it was claimed he stormed out of a meeting with club officials this week when a proposed loan move was blocked due to injuries to senior players.
"I can only tell you I had a 30-second chat with him on the training pitch today and there was nothing like that at all," said Moyes.
"I had said if I couldn't get him games, I'd put him on loan.
"But he can't go out loan while I've got Ashley Young and Nani out injured.
"I'm surprised anybody was even thinking about that as a possibility."