I think so. but I don't think you need to get through customs if you're there for transit. you should inquire your airline for details so you don't get lost.
If you mean screenings, yes you need to go through that & transit procedures. read here if your transit is in Narita http://www.narita-airport.jp/en/guide/connect/inter/index.html
my experience in Narita was satisfying. they're really good in making time more efficient, from distributing people queue on immigration to quick & easy & friendly customs.
If you're already here, welcome to Java! almost 5 years ago