Rooney, 27, missed the 4-3 win over Newcastle United at Old Trafford on Boxing Day after suffering a knee injury during training on Christmas Day. The England international also missed United's next two fixtures against West Brom Albion and Wigan Athletic.
The England striker will now miss the clash at Old Trafford against fierce rivals Liverpool as well as the FA Cup battle against West Ham on Saturday.
Meanwhile, manager Sir Alex Ferguson was surprised to hear about Rooney's injury but said there was nothing serious.
"Wayne Rooney is still injured. It's a bit of a surprise because it's longer than we thought. We expected him to be back in training but he's not," Ferguson said.
"It's nothing serious but it looks as though he's going to be out for another two weeks or so. He won't be set for Liverpool. He just got clipped behind his knee. We sent him for a scan and nothing really showed but he's still feeling it," he added.
Despite being in great touch, Ferguson always wants to field his best players.
"Although we're in great form you always want your best players available for games that are coming up. We've got West Ham tomorrow, Liverpool next week and then Tottenham the week after that. And the FA Cup again hopefully after that," Ferguson said.
However, there was some good news for United with Nani, who has been missing from action since two months with a hamstring problem, set to start training on Friday.
United have had injury problems at the back but that seems to have gone and their main strength lies in attack, winning eight out of their last nine Premier League games.
The Red Devils are currently on top of the table with 52 points, seven points clear of title rivals and defending champions Manchester City.