@Fushan - the crossover would be entertaining.
I think the author is attempting to balance "trust in government" and "distrust in government" viewpoints. The main characters are clearly trying to convince themselves that the government's wariness toward epidemic and magic are legitimate, and that their methods (arrest, property seizure/possible destruction in all but name) are legitimate. I get the idea the native Japanese citizens don't really believe that, but don't want Chris to panic or prompt the govvie to take a more... effective action. The way the government agents are portrayed is unsettling (faceless, silent, hardly seeming human), and Chris is being courageous in putting on a brave front in going with them.
I'd actually say the author is straying too far into the "don't trust government, they're evil" - if he'd had one of the characters say/think something in the vein of "Governments are legitimate in that they have a monopoly on the violence to enforce their legitimacy," I'd have rolled my eyes.