The striker, who has been short of form and goals all season, was substituted with half an hour left against Bolton in the Barclays Premier League on Sunday after injuring his ankle and did not travel with the United squad for their Champions League match against Valencia.
The injury update from Ferguson means Rooney will miss the game at Sunderland on Saturday and also England's Euro 2012 qualifier against Montenegro on October 12.
Blow: United and England striker Rooney is facing three weeks out of action
Rooney's absence against Montenegro will be a blow to Fabio Capello given he has already lost Frank Lampard, Theo Walcott, Jermain Defoe and Bobby Zamora in a growing injury list, plus James Milner through suspension.
However, it could be argued it is just what Rooney needs after an awful period, during which time his private life has been thrown into turmoil and his form has collapsed.
He has still only scored once this season - from the penalty spot - compared with three in a week for Michael Owen and seven so far this season for top scorer Dimitar Berbatov.
Blow: Alex Ferguson watches on as Rooney is subbed at Bolton
Former England skipper Kevin Keegan claimed on Sunday that Rooney's confidence was 'shot', adding the forward only had himself to blame for the press intrusion into his life because of the number of endorsements he current has.
Not that Ferguson was getting into such topics this evening.
'It is a straightforward ankle injury,' he said. 'And it is not the same one he did in Munich.'
Ferguson also confirmed that midfielder Paul Scholes will be sidelined for 10 days with a calf problem.
Rooney's form collapse can be traced back to that injury in the first-leg of last season's European quarter-final against Bayern Munich.
Ferguson has previously insisted he did not rush Rooney back too quickly, although he will hope when his star man does return from his present lay-off, he is more like his old self than the shadow player he seemed to have become.
"Nobody likes to be injured but he is. There is nothing you can do about it,' said the United boss.
Unfortunately for the Red Devils, Rooney's is not the only injury for them to contend with.
Although it was assumed Scholes had simply been rested after completing the full 90 minutes against Bolton at the Reebok Stadium, Ferguson has revealed the 35-year-old has instead picked up a niggling calf problem.
'You don't want to lose your best players, that goes without saying,' said Ferguson. 'The problem is with one of those small injuries like Paul has got, when you are travelling and sitting on a plane, stiffness comes into it and doesn't make it any better.
'It was a big decision to leave him behind. Because it is only a little one, you are tempted to play him when it is not wise. He should be ready in 10 days.'
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