The US military has guides for its personnel with advice on what to do to get to their destinations in japan:
http://www.militaryinstallations.dod...f?p=MI:ENTRY:0

Type in the name of any US base in Japan to open the relevant guide. The "directions" section (click "directions" in the left side menu) provides information on airport arrivals. When I looked up Kadena AB (in Okinawa) it lacked specific information about arrival at Narita, but if you look up Misawa AB, it's quite detailed.

As far as I can see, the process for military personnel arriving at NRT is not so different from civilians, except the visa status is different.

Hope this helps.