Rooney will miss England's September Euro 2008 qualifiers after suffering a hairline fracture of his left foot on Sunday.
Ferguson believes Rooney will be out until October after the 21-year-old was injured in the Premier League opener with Reading.
"We expect him to be out for two months," said Ferguson.
That rules Rooney out of the key home matches against Israel on 8 September and then Russia four days later.
Ferguson added: "To be on the safe side, we would say it is going to be two months but hopefully he can come back quicker.
"It's a bad blow for England and I'm disappointed for England coach Steve McClaren. I spoke to him last night and I could sense the disappointment. It is a bad blow for him.
"They have options for the games against Israel and Russia in September. They should cope without him. I would expect him to be back for October."