The 25-year-old missed out on United's 1-1 draw with Stoke City yesterday because of a hamstring strain.
The in-form England international could now miss Tuesday's Champions League tie against Basel and Saturday's Premier League fixture against Norwich.
"It's not a serious hamstring injury but I don't think he'll be available for next week," Ferguson said. "I think he'll be out for more than a week."
Rooney has been in clinical form for United this season, scoring nine goals in all competitions - including Premier League hat-tricks against Arsenal and Bolton Wanderers.