The United veteran has been struggling with the problem and sat out the midweek trip to Real Madrid.
And Ferguson revealed Scholes will not be available for Monday's FA Cup tie with Reading.
"It is a knee injury, which has been bothering him a bit," said Ferguson.
"We have tried another treatment during the week.
"He will probably be back in another couple of weeks."
Ferguson confirmed his squad had come through their midweek exertions without a problem, but that there would be changes to his starting line-up against Brian McDermott's progressive team.
"I will make some," he said.
"We want to get to the quarter-finals and we do expect to qualify."
Ferguson also had words of praise for David de Gea, who produced possibly his best performance for United in the 1-1 Bernabeu draw with a string of fine saves.
"He is maturing," said Ferguson. "Very few goalkeepers go into the first team at 20. Gianluigi Buffon and Petr Cech are two examples of those who did but it is not always the case.
"Peter Schmeichel didn't join us until he was 27, and he gave us eight great years."
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