Hughes saw City crash to a 3-0 FA Cup defeat to Nottingham Forest on Saturday.
But chief exec Garry Cook said: "Mark is part of building the club, from the playing side right through to making this a great place for employees.
"What we don't do is sit around worrying about what happens if it goes wrong."
Cook moved swiftly yesterday to back his beleaguered manager following one of the biggest cup upsets in recent seasons.
He added: "Once we get through the first window, when Mark's impact will be able to advance the future of the football club, things will start to settle down.
"Mark's plans and the way he is running the team are going to build and change and the confidence will start to build.
"We will bring people here who want to see the club move forward and the fans will ideally take to them because they're committed to the club."