The former Celtic and Southampton left-back has been out since October but the injury is failing to respond to either treatment or rest.
"If things don't work out he might need an operation which will be a massive blow," said Kevin Blackwell on the club's official website.
"At the moment I have to play it by ear but it does not look too good for Stephen.
"If Stephen is going to be out for a long length of time then I would have to look at bringing someone else in."
However, Seth Johnson may be back sooner than expected. The 25-year-old is in the final throes of recovering from a cruciate injury and, barring any slip-ups, will begin full training with the squad next month.