What would you do if some staffs kept complaining?

I wondered what you would do of being a boss if some staffs kept complaining where there had been lot more of non-cooperations between departments, but those of complaining could only take orders from yourself but not from the managers. And this is where the work-flows-from-department-to-department could be on setback......and more insufficiency being remained in place where the firm itself is in problem-dissolving situation.........any professoinal advice......