The former Leeds United and Wigan Athletic man suffered an injury during Saturday's 4-1 defeat to Hull City at the KCOM Stadium.
Warnock went down after he made a run forward and he seemed to suffer the problem while trying to cross the ball.
He managed to carry on for a short while before being replaced by Lloyd Dyer and the club's fans were hoping to see him in action in midweek.
However, Clough has confirmed he is struggling and will miss the trip to Boro on Tuesday evening.
Clough told the Burton Mail: "No, no - it's too early (to tell) at the moment, we'll know a bit more early next week.
"He'll certainly not be available for Middlesbrough."