The Hoops captain's future is in doubt after he elbowed Carlos Tevez, kicked Sergio Aguero and appeared to headbutt Vincent Kompany during Rangers' 3-2 defeat at the Etihad Stadium on the final day of the season.
"We are waiting to hear on Joey Barton's punishment," the Rs boss told the Daily Mail. "He is facing a long ban and we have to take stock of the situation."
Barton has accepted a charge of violent conduct against Aguero but denied the same charge for his confrontation with Kompany, while QPR have announced they will conduct an internal investigation into his dismissal and subsequent conduct.
Reports earlier this week suggested the west Londoners would consider trying to offload - or even sack - Barton, who has three years left to run on his contract, but Hughes pledged not to make any rash decisions.
He added: "We are awaiting the verdict of the FA and the disciplinary process will take its course. As a manager there are 10 other players you have to think about, then 10 who played on against Manchester City.
"We stayed up. It's a relief. And now we start again. This is not all about Joey Barton."
The west Londoners stayed up at the expense of Bolton and are now looking to a brighter future.
Plans for a new state-of-the-art training complex were announced this week and Hughes wants to bolster the squad over the summer in a bid to make QPR an established Barclays Premier League club.
"When I said no team of mine will be in this position again I meant it," the Welshman said. "Since we've been in the building it has been about creating the standards and behaviour we expect. Now we are ready for the next level."
Source: PA
Source: PA