Rooney injured the ankle in the 2-2 Premier League draw at Bolton Wanderers on Sunday and will miss Wednesday's Champions League Group C clash at Valencia and the Premier League match at Sunderland on Saturday.
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"Two to three weeks maybe it depends," Ferguson told a news conference at Valencia's Mestalla stadium when asked how long Rooney would be out.
"He's a strong lad and he's done quite well in recovering from injury in the past," he added.
England international Rooney had a disappointing World Cup in South Africa and has yet to rediscover his best club form following widely-publicised allegations about his private life.
Asked how the latest injury setback was affecting the player's state of mind, Ferguson said: "Nobody likes to be injured. I think he'd rather be out here playing with us but he's not. There's nothing you can do about it."
Rooney is also likely to miss England's Euro 2012 qualifier against Montenegro on October 12.
United midfielder Paul Scholes has a calf injury and Ferguson said he should return to action in around 10 days.
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