Rooney sat out Monday's FA Cup defeat of Reading with a sinus problem, and although the 27-year-old has now returned to training, Ferguson feels it is unlikely he will be available at Loftus Road.
"He came in for the first time yesterday and the medical people are dealing with him," said the United boss. "He has been on medicine and hopefully he will start training today, but I wouldn't think he would be available on Saturday."
If Ferguson's assessment is correct, it would mean Rooney will have missed two-and-a-half weeks of action by the time United are next due to play, against Norwich at Old Trafford on March 2, just three days before the second leg of their Champions League encounter with Real Madrid.
As Ferguson has repeatedly said Rooney needs matches to maintain his fitness, it may provide the United boss with an unwanted selection dilemma in addition to that surrounding Phil Jones, who only has an "outside chance" of being fit after suffering an ankle injury on Monday.
Meanwhile, Ferguson insists he wants to keep Nani, but warned the winger his performances will dictate whether he gets his wish for a regular first-team berth.
Although he initially flourished following Cristiano Ronaldo's world-record transfer to Real Madrid in 2009, for the past 18 months Nani's influence on United has started to wane. There have also been wranglings over contracts, with the Red Devils apparently unwilling to offer the Portugal international the kind of terms he wants.
With 18 months left on his present deal, Zenit St Petersburg made an inquiry during the recent transfer window, whilst the completion of Wilfried Zaha's move from Crystal Palace next summer has been viewed as a clear signal of impending departure. Yet Ferguson insists he would be a reluctant seller.
"I would definitely prefer to keep him until the end of his contract," said the United boss. "He is one of the best match winners in the game - and I am including the whole of Europe.
"He has scored the most incredible goals. The boy has a talent for winning matches. We have been speaking to his agent for quite a few weeks now but it is entirely up to the boy himself."
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