The former England striker has been ruled out for the majority of the season with an anterior cruciate ligament injury picked up against Chelsea last weekend.
"We're upset obviously for Andy and for ourselves as a club and as a team," Hughes said.
"He showed us in his time with us why we brought him to the club, with the qualities that he has. Unfortunately, we are not going to be able to use those qualities for a significant amount of time.
"His energy and his undoubted ability will be a loss for us but obviously you build your squad so you can cope when you have long-term injuries.
"The absence of Andy will allow other players to come to the fore, I am sure."