Rooney has missed the last three United games after sustaining a training ground injury on Christmas Day as he damaged a ligament when volleying the ball.
He had initially been ruled out of the festive programme, and this weekend's FA Cup third-round tie against West Ham, but will now also be absent for the match against Liverpool at Old Trafford on January 13.
"Wayne's still injured, and it looks like going to be out another two weeks or so," Sir Alex Ferguson said.
"It's a surprise as he was meant to be back training now. So he'll be out for longer than we thought and I don't think he will be fit for the Liverpool match.
"The injury is nothing serious. He just got clipped behind his knee. Nothing shows in the scan but he's still feeling it. Hopefully in two weeks it'll be sorted but nonetheless it's a loss."
However, defender Phil Jones is fit for the cup tie with West Ham and Nani will return to training on Friday, even if Darren Fletcher may not feature at the weekend if the conditions are not favourable.
"The ground has been really heavy recently and I don't think the pitches have suited him," Ferguson said. "I've explained that to him.
"But we're in good shape now with good options. We've utilised the squad very well in the last few weeks."