The striker, who has been the subject of two failed bids from Chelsea after reportedly handing in a transfer request, looks unlikely to face Wigan due to a shoulder injury.
The England international has missed most for the club’s preseason preparations after a hamstring injury saw him return home from the club's tour of Asia, before he damaged his shoulder in a behind-closed-doors friendly against Betis.
Rooney, who was the subject of a rejected bid from Chelsea worth nearly 30 million pounds over the weekend, is also a doubt for the Three Lions’ friendly with Scotland on Wednesday, but Moyes remains faintly hopeful of his inclusion against Wigan.
"I don't think he is going to be fit and available. Of course we are still hoping he will, but I have a feeling he won't make it," Moyes told reporters.
The involvement of Jonny Evans and Nani is also in question after the pair limped out of the 1-1 draw with AIK on Tuesday, but Moyes is more confident of being able to call upon David de Gea and Mexican star Javier Hernandez for Rio Ferdinand’s testimonial against Sevilla on Friday.
"Jonny Evans actually got kneed on the ankle. He thought that he was going to be able to run it off, but if we left him on then it would only have got worse for him," Moyes said. "Nani just felt his groin tighten up and he didn't want to take any risks. Neither did we. We thought it was safer to take him off at that time. Most of the injuries we have got are not serious, we are just protecting them.
"David has hurt his finger - but he's okay. He could have played in Sweden and we hope he will be fit for Friday night and Sunday's Community Shield against Wigan at Wembley.
"Javier has a bit of a hamstring problem that he picked up in training, but we didn't want to risk him."