The 27-year-old did not travel to Sweden for United's 1-1 friendly draw against AIK Solna on Tuesday night because of an injured shoulder but visited Carrington briefly in the morning before leaving just before midday.
Several newspapers claim the England forward is facing a dressing-room revolt over his alleged desire for an Old Trafford exit.
United seem intent on clinging on to Rooney after rejecting a second bid of around £30m by Chelsea and new manager David Moyes insisting over the last few weeks that the forward was not for sale.
"Wayne hurt his shoulder in a fall during a match on Saturday," Moyes told the United website. "It's not too serious and I don't expect it to keep him out for too long.
"I'm disappointed he's missing the game because we were keen to get him back involved and ready to play."
After another friendly against Sevilla, the Premier League champions will begin their defence on August 17 at Swansea six days after playing Wigan in Sunday's Community Shield at Wembley.
However, with four weeks left in the transfer window, Chelsea boss Jose Mourinho will be carefully weighing up his options as he considers making his next move to snare Rooney.
The former Everton star has two years left on his current deal at United and is reportedly ready to force a transfer through by handing in a written transfer request.
On Monday, a United spokesman reiterated the club's defiant stance and said: "A bid was received on Sunday and immediately rejected. Our position remains that he is not for sale."
Nemanja Vidic will skipper the United side in Sweden after missing the first leg of the tour due to a sciatica problem, while Portuguese winger Bebe, signed for £7.4m in 2010 but yet to start a game in the Premier League, is also in the squad.