Rooney, who signed a new five-year contract at Old Trafford last week after first shocking the club
by saying he wanted to leave, is currently on holiday recovering from an ankle injury.
When asked at a press conference Friday if three weeks was still the prognosis for his return, Ferguson said: "I think it may be longer."
Rooney was injured in training last week following a challenge with team-mate Paul Scholes.
The 25-year-old has since been given permission to travel to Dubai to recuperate and celebrated his birthday there with wife Coleen last weekend while United were winning 2-1 at Stoke.
Ferguson has no plans to rush Rooney back and he believes a longer than expected period of rest is the best cure for the England striker.
"There is no recovery, it is just rest," Ferguson said. "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 appeared to be on his way out of Old Trafford last week when he criticised the club's lack of ambition.
He was eventually persuaded to stay after being handed a massive wage increase, while the Glazer family, who own United, made personal assurances that there would be increased investment in new players.
Rooney's prolonged absence puts pressure on Bulgarian forward Dimitar Berbatov and young Mexican striker Javier Hernandez to lead United's attack until he returns to fitness.
"We are all pleased with Javier," admitted Ferguson. "Everyone's excited by him at the club. He's done really well.
"He's got the right desires and trains very well. He's very receptive to coaching and has a good pedigree.
"He's a young boy who has come from Mexico and a different culture. But he speaks the language which is important.
"We are not surprised as we identified a lot about him before we signed him. We did a lot of work on him. Therefore after seeing him in the pre-season and in training, we thought he would do well."
Although Rooney has been out of form this season, scoring just once for United, he will still be sorely missed at a time when United forward Michael Owen also faces an extended spell on the sidelines.
Owen was hoping to return from a groin strain in the midweek League Cup tie against Wolves but suffered a hamstring injury in training, which will keep him out for several weeks.
Ferguson said: "It is disappointing for him (Owen). 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."
Meanwhile, United midfielder 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 England midfielder Hargreaves would be ready to take a place on the bench soon after a long battle with the knee problems that have sidelined him for 18 months.
Hargreaves, 29, has not started a game since September 2008 and 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."
Ferguson's team, who host Tottenham on Saturday, are currently five points behind Premier League leaders Chelsea.
You have to back to 1989 - a staggering 20 matches ago - for the last time a Spurs side won at United. But Ferguson is aware that run could be ended by Harry Redknapp's improved outfit.
"We are seeing a new Tottenham over he last couple of years," he said.
"I think there progress has been excellent under Harry. He's brought a consistency to them.
"The area which is to new to them is coping with playing in the Champions League and the Premier League."
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