The unsettled forward has not played for United in pre-season due to injury and is set to miss Sunday's Community Shield against Wigan.
But he has still been called up by England manager Roy Hodgson for the friendly against Scotland next Wednesday.
However, Hodgson is adamant the Rooney situation will not cause a problem between him and Moyes, and the United manager concurs.
He told MUTV: "I had a long conversation with Roy about it last week.
"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."