Ferguson added: "That's Fabio Capello's call and how he progresses in the next few days but I have no problems with that."
England host Kazakhstan on 11 October and travel to Belarus four days later.
A United spokesman told the club's website: "Wayne has an ankle injury and is doubtful for Saturday, but he should recover in time for England's forthcoming matches."
Ferguson will be relieved Rooney has not suffered ligament damage as he will already be without influential midfielder Paul Scholes for 10 weeks.
Scholes, 33, damaged his medial knee ligaments in the same game and was stretchered off after only 16 minutes in Denmark.
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