Rooney, who signed a new five-year contract at Old Trafford last week, is currently away resting after suffering an ankle injury.
When asked at a press conference today if three weeks was still the prognosis, Ferguson said: "I think it may be longer."
Rooney, 25, was injured in training last week during an extraordinary few days that ended with him committing his future to the club after previously stating a desire to leave.
He has since been given permission to travel to Dubai to recuperate.
Ferguson said: "There is no recovery, it is just rest.
"Before he went away we did his remedial in terms of what we could do at the time. Thereafter, rest - we're quite happy with that."
Rooney has struggled for form this season, scoring just once for United. His absence has reduced United's frontline options with Michael Owen also facing an extended spell on the sidelines.
Owen was hoping to return from a groin strain in the midweek Carling Cup tie against Wolves but pulled a hamstring in training.
Ferguson said: "It is disappointing for him. It should be four or five weeks.
"The last thing he needs is a hamstring injury.
"It is a loss because with Wayne being injured it only gives us the three options at the moment."
In their place, Javier Hernandez has impressed with four goals in four games while Dimitar Berbatov shone in the opening weeks of the campaign. Federico Macheda is Ferguson's other forward alternative.
Veteran Ryan Giggs is set to return to training on Monday after a fortnight out with a hamstring injury but Owen Hargreaves remains some way off a return.
United had hoped the former Bayern Munich midfielder would soon be ready to take a place on the bench after a long battle with knee problems.
Ferguson said: "He was making very good progress when he first came back but that seems to have stalled a bit and he is back with the physios now."
Hargreaves, 29, has not started a game since September 2008 and has made just one brief substitute's appearance - towards the end of last season - in that time.