Basic principle governing the Trademark Law of Japan is “trademark registration is a prerequisite for protection”,”the first to file prevails” and “Administrative examination by JPO is a sole route to obtain trademark registration”.
Since Japan is a member state of the Madrid Protocol, you have two options in registering your trademark in Japan. One is to file a trademark application directly to JPO, the other is to initially or subsequently designate Japan in filing an international registration through the WIPO. Application via the Madrid Protocol occupies about 10 % of new trademark application filed to JPO in a year (147,283 new applications in gross in the year of 2015).