Japan marriage

Hello Itsnil:   If I understand correctly, your fiance is in the U.S. military....stationed in Japan.   If so, start with him.   He has to check with the JAG (they handle legal matters in the military) on the legal aspects of marriage with a foreign national.  Then he has to get with the Chaplain on base to coordinate the wedding event...if that's case...that is if you two decide on a church wedding.  Depends on his military grade...your fiancé's commander might also be involved in the process.  I remember as a young buck private stationed in the U.S. Army in Manila, I wanted to marry my girl friend and had to get my commander's permission and blessing.  It's like the commander acts as a parent.  Which is a good thing of course.
I am not sure if they still do that in the military these days.   So check with your fiancé and let him handle the process...a sure way to know (rather than asking expats) for sure as the procedure may have changed.  Good luck.