I very much got a 'ragtag bunch of survivors' vibe there, like, they are taking what they can get, manpower shortages are mentioned etc. I don't think there IS government anymore, aside from enclaves of survivors being run as citystates.
Except that the Wunder is fleet is made of dozen of aircraft carriers, cruisers, destroyers, submarines, cargo ships... enough ships to put to shame all of the US Navy Pacific Fleets, and then there's the AAA Wunder itself, who's a whole fleet by itself. You just don't maintain such a gargantuan fleet in a Fallout-like scavenging supply routine.
Hell, the first scene with the fleet had a huge fleet of choppers delivering cargo to the naval fleet, if that's not an indication that there's some serious supply chain organization going on in behind the scenes.
So I wouldn't be surprised if there are other branches of WILLE around the world, and even higher-ups Misato has to respond to.