Rooney sustained a minor knee injury in training on Christmas Day and Sir Alex Ferguson initially expected the striker to be back in a fortnight.
However, it now seems he will be missing for longer - and will sit out next week's clash with Liverpool.
"Wayne is still injured," said Ferguson.
"It is not serious but it is going to take longer than we thought, probably another two weeks. He won't be fit for Liverpool."
Rooney was expected to have been back in training by now and Ferguson cannot exactly work out why it has not happened.
"He got a little kick behind his knee and he is still feeling it," said Ferguson.
"Hopefully another couple of weeks will sort it out.
"Nonetheless, it is a loss. You always want your best players available."
There was some good news, though, with Ferguson revealing winger Nani, who has been absent for two months with a hamstring problem, will take a major step forward in his recovery.
"He starts training today [Friday]," he said.
Ferguson also explained the reason behind Darren Fletcher's recent absence.
After battling back from a chronic bowel condition, Fletcher played four times in a fortnight at the end of last month.
However, the midfielder's only appearance since came as a last-minute substitute in the Boxing Day win over Newcastle.
"The grounds have been really heavy, which has not suited Darren," said Ferguson.
"The pitch at Old Trafford seems to have collapsed in the last two weeks.
"We have had six great years out of it. They have done a fantastic job but we are going to have to change it during the summer."