He returned as a second-half substitute in the Johnstone's Paint Trophy defeat at Rotherham on Wednesday but went off after only 10 minutes.
Gary McAllister said on the club's official site: "He's struggling now, he'll probably be out for a while. We needed to see if he was fit, he did it a few weeks ago, but due to his absence through suspension, it gave him time to get the hamstring right. He has been training for a good few days now but he broke down again so that's a big blow to us."