Office of Personnel Management

Can your supervisor be in a different department/flight (Air Force)? I belong, officially on paperwork and unit manning document, etc., to one flight but a flight commander for another flight self-appointed themselves as my supervisor. Can this be done? Our local RMO said they could, but they don't always do stuff by the rules at my location and this just doesn't seem right.

Depends. If your current flight commander hasn't taken the training to be a supervisor for civilians, and the other one has, this may be the reason (also, could be to keep all the civilians under one supervisor for consistency in appraisals, etc). Could be your flight leadership has had issues supervising civilians in the past...and so on. Is your flight commander military and the other one civilian? Both military? Both civilian?

Your situation is not common, but not unusual in a military environment. See it in Wing Staff offices a lot as they are small and the mil and civ in the same office may technically be vertical on the org chart, but in reality the civ may be equal or higher in protocol grade (ie, a Captain or Major is the office chief, but the civilian is a GS12 or 13) and as the mil changes out frequently, it is easier to keep the civilian's supervisor as a senior civilian on the wing staff who is likely to be in another office.