The 20-year-old returned to the side following a six-match absence to produce a starring performance as Hibs lost out to Celtic.
However, Hanlon continues to battle the pelvic problem which has plagued him over the past few months and, with Sol Bamba suspended for the next three games and skipper Chris Hogg still struggling to overcome a back injury, Hughes is taking no risks with the Scotland Under-21 star.
Revealing Hanlon won't be asked to join in team-mates in training until tomorrow as they prepare for Sunday's showdown with Rangers, Hughes said: "I thought Paul did a great job in defence against Celtic, especially when you consider he had only trained twice before the game.
"That'll be the case again this week, wrapping him up in cotton wool because of the kind of injury it is, you've got to be extremely careful with pelvic problems.
"It's a bad injury that he has got and you've got to work it, rest it, work it, rest it, it's the only way to deal with it.
"A lot of the time these kind of injuries can be caused by the change in the surface, going from the hard ground to the soft ground when the weather changes.
"If you keep battering away at him and pushing him all the time then you can make the situation even worse so we have got to watch what we're doing.
"I have got to take my hat off to him though because, prior to the game against Celtic, he hadn't played a single game in six weeks and had only trained with the rest of the team twice. David Wotherspoon was the same and you've got to give these young boys credit.
"It's going to have to be like that between now and the end of the season because we've got suspensions and injuries to deal with.
"It's a massive bonus to have him back in the side because, to be honest, I didn't think that we would have him available again this season."