After Sunday's win over Aston Villa United boss David Moyes claimed officials were not doing enough to protect the young winger.
"It's terrible what they (opponents) are allowed to do to him at the moment because this boy's an incredible talent. It's for the referees - that's their job," the Scot said.
Hughes, however, believes the 18-year-old needs to toughen up, and while he did not go as far as accusing Januzaj of diving, he highlighted the number of fouls the player seemed to win in their encounter at Old Trafford in October.
"A manager will always protect his players and he is an outstanding talent and will be a top United player for many years to come," said Hughes ahead of his former club's visit in the quarter-final of the Capital One Cup on Wednesday.
"If David feels the boy needs protection that is why he has given the response he did, but you have to let kids stand on their two feet and get on with it.
"He seems to garner a lot of fouls and a lot of decisions. In our game he came on as sub and got about five fouls in a very short space of time. At the time I didn't think they were fouls."
Hughes pointed to the grounding United veteran Ryan Giggs had early in his career, which appears to have done him no harm as he continues to play past his 40th birthday.
"Ryan was playing in the Lancashire A and B leagues and had to go to the likes of Marine away," he said. "When you are a 14-year-old kid coming up against men you learn to deal with that early and I don't think it is a bad thing.
"I would imagine he (Giggs) is mentoring him now because he's been in the same place."
Moyes has come in for criticism after suffering five Barclays Premier League defeats this season, including some surprise home losses, which has left them well off the pace even in the race for Champions League qualification.
One of the accusations is that the Scot's tactics are too negative, and while Hughes accepts there is a certain style of play expected from United, he believes opponents have sensed a chance to challenge the established order.
"There is an expectation for United teams to play in a certain way but you have to give the opposition credit," he said.
"This year a lot of teams have gone to Old Trafford certainly thinking we're going to have a go and see what happens and have been encouraged by the success they've had and we include ourselves in that [Stoke lost 3-2 at Old Trafford in October].
"It is probably a change in attitudes from opposition teams which has put United on the back foot."
Moyes spent 11 years at Everton without winning a trophy but his Stoke counterpart said he did not think that would cloud his judgement when it came to assessing the importance of the Capital One Cup.
"You'd have to ask David yourself but he's not won any silverware in his own right so I guess that figures in his mind - but he would always prioritise the trophies United would be expected to win," he said.
"You wouldn't put personal ambition before the club's ambition, I wouldn't suggest that for a moment, but if I was in his place I would go strong."