Hughes suffered a groin injury against Wolverhampton Wanderers earlier this month, and Clough has refused to put a date on when he expects the 17-year-old to return to County's side.
Clough told reporters: "There has been no real improvement in the injury and, as much as we want Will back on the pitch, the bigger picture comes into view. We have to make sure he is right.
"If he was a 28 or 29-year-old professional, we would be patching him up and getting him back on the pitch. But we do not want any long-term effects.
"We will give him as long as he needs and we will make sure he is right."
Hughes has made 35 appearances for Derby this season.