Having failed to make any appearances during pre-season, unsettled striker Rooney will also be absent when United take on Wigan in the Community Shield.
But the minor shoulder injury that prevented Rooney from travelling to Sweden last week has not stopped him from being called up by Roy Hodgson for England's friendly with Scotland on Wednesday.
And a pointed statement from Rooney on his official Facebook page on Friday night, which thanked Hodgson for the faith he had shown in him while omitting any mention of Moyes or United, was taken as further proof that all is not well.
However, while the position is far from ideal given Rooney's desire to leave and his time spent training with the reserves this week, Moyes has indicated the rift is not quite as bad as some have claimed.
"I had a long conversation with Roy about it last week," Moyes told MUTV.
"Wayne has had a shoulder injury. He has been sore with it, which has meant he has not been able to have any contact, so he hasn't trained with us [the first team].
"He has trained a little bit with the reserves as a non-contact player, a floating player, so at least he got a little bit of football work.
"He trained with the first team today [Saturday] and he did a bit of extra work, so he is probably more likely to be ready for England than he will be for us.
"You've got to remember he has had no football practice.
"I explained all this and I would only expect Roy to play him for a short time."
Moyes' version of events tallies with Hodgson's, who is keen not to be seen as profiting at the new United manager's expense.
Speaking to Sky Sports News, Hodgson said: "The only problem is that my selection of him could be used as a wedge between David Moyes and myself.
"There's not going to be any wedges put between us two, we've been friends for a very long time. David understands fully the situation.
"David knows what we have in mind and unfortunately we just have to accept that there'll be some opinions on the subject and that people will try to drive wedges, but it's wrong to do so."
Hodgson's assistant Gary Neville added: "It will have no effect whatsoever on the England squad.
"I've played with Wayne Rooney for many years and I've been coach with England for the last year and a half. I've never seen him give anything other than 100 per cent in every single training session.
"It's an insult to suggest he would have any negative effect on any England squad.
"He's not that kind of lad. He's a good lad, a great player, a fantastically important player - not just for Manchester United but for England.
"We'll just concentrate on looking after all the players. Wayne Rooney will come along and do his very best as he always does."
Rooney, though, will not be involved when United search for their first trophy of the Moyes era against Wigan tomorrow.
Neither will Nani, nor Ashley Young, who have both also been ruled out of a fixture United could really do with winning given their troubled pre-season.
"[We will] take just about everyone that's fit. We are one or two short, likes of Nani, Ashley, Wayne are not available for the game at Wembley," Moyes said.
"Apart from that nearly all others players, if everything goes well, are fit and available to travel.
"It's a really important fixture because it's the start of the season for us."
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