The United forward is expected to be fit to face Real Madrid, but the QPR match could come to soon after the striker picked up an illness.
He's missed the majority of this week's training, and reportedly won't travel to London for the meeting with the Premier League's bottom club.
United's in-house TV channel MUTV reported Rooney's complaint, while Sir Alex Ferguson confirmed Phil Jones faces a race against time to recover from injury in time to face Real Madrid.
A win over relegation-threatened QPR could send United 15 points clear of title rivals Manchester City. Roberto Mancini's men welcome Chelsea to the Etihad Stadium on Sunday afternoon - but by that time United may have already extended their advantage.
United will hope Rooney overcomes his problem in time to face the La Liga champions in the second-leg of their Champions League last-16 encounter.
A 1-1 draw from the first-leg was thanks in part to a disciplined performance from Rooney and Danny Welbeck on the flanks, and Rooney will no doubt be hoping to show what he can do in a more attacking role in the home leg.
Ferguson also confirmed Jones, who hobbled off against Reading in the FA Cup on Monday night, has a slim chance of playing against Madrid at Old Trafford.
The England international did a superb job shackling Cristiano Ronaldo for much of the game at the Bernabeu, and if fit he could be expected to reprise that role for the Old Trafford tie.