In the most basic sense, the cradle to grave responsibility for the weapon system falls upon the Program Manager (PM); however, the Product Support Manager (PSM) is responsible to the PM for the Product Support Strategy/Plan, which includes all Supply Support.

The inventory quantities are determined using an algorithm which takes into account Concept of Operations of the weapon system, the design characteristics of the weapon system (failure modes, failure rates, time to repair, etc.),  and the availability requirements, to name a few.  Much of this data becomes available during the Engineering and Manufacturing Development Phase (EMD), though it could be earlier or later depending on program specifics. 

In most cases, the service's primary supply management function maintains the program providing the calculation.  I note the originator of this question is from the Navy, so consider contacting NAVSUP, Mechanicsburg (PA) for NAVSEA support and Philadelphia (PA) for NAVAIR support.

I hope this helps, if there are any particulars to discuss, please feel to contact me.