As much as Clough admits the Rams are missing the teenager, he has already ruled the midfielder out of the next two matches against fourth-placed Crystal Palace at Pride Park on Friday and away to Championship leaders Cardiff on Tuesday.
Hughes missed his first game of the season against Bolton on February 19 after injuring his groin against Wolves in the previous fixture. The 17-year-old remained sidelined for Derby's defeat at Watford last weekend.
Clough has not put a timescale on when his prized-asset, who has been watched by several Premier League clubs this season, will be back - only insisting it will not be until he is fully fit.
"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," Clough told reporters ahead of the visit of Palace.
"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."
Clough added: "We missed Will at Watford, as we did against Bolton. Watford was the sort of game where you wanted somebody to get a foot on the ball and create, or thread a pass through."