Hughes came off the bench to play five minutes against Peterborough on Saturday after missing more than two months with a groin problem.
The teenager's injury was more serious than first thought and Clough has hinted he may now wait until next season before fully re-introducing Hughes to first-team football.
Clough said: "It was more serious than a groin strain, it was a stress injury. You cannot put a time on such an injury so we must still be careful with him.
"We are still not sure if he is going to feature much more before the end of the season.
"The main thing is that he goes into the summer fit, works over the summer and comes back fit for pre-season training."