Have you ever tried to add a navigation controller without starting up a project based on that controller?
Well you can’t have such project on iPad as well.
So after some Google you find something like this solution:
http://johnnytrops.com/blog/wp/?p=224

Another way is to drag the Navigation Controller in Interface Builder to the XIB, specify it’s RootViewController class, and assign an IBOutlet property in the File’s Owner (can be app delegate or another ViewController).