The Scot told local radio station Key 103 that, although the striker was eager to make an immediate comeback, Rooney's ankle injury needed time to heal and the striker would miss United's trip to Sunderland in the Premier League on Saturday.
"Wayne trained yesterday and wants to play tomorrow of course," said Ferguson.
"But I've got to take the view that this ankle injury has been niggling for quite a while and he has kept on playing with it. Now we have identified that, we have to be dead sure we are doing the right thing for him.
"He has been playing with the injury for a while and that tells you he is not doing himself proper justice. I think in another week he will be fine," said the United manager.
"Obviously, we don't play next week, but the England game is a week on Tuesday, so that's another 10 days. It really is up to Fabio (Capello) if he wants to play him."
Ferguson told reporters in Spain on Tuesday that Rooney would be out of action for up to three weeks after injuring the ankle in the 2-2 draw at Bolton Wanderers last Sunday.
The player scored his first international goal for almost a year earlier last month when England beat Switzerland 3-1. They have maximum points in Group G.
United's next match following this weekend is against West Bromwich Albion at Old Trafford four days after England's home game against Montenegro.
"The problem with the lad is that he is too willing to play with injuries," said Ferguson. "It is a great trait to have in any footballer.
"I have had many players over the years who might have had injuries but weren't prepared to miss a game because of them.
"But with the speed and number of games you have these days, fitness levels are really important."
