Judge for yourself.
Same company, same job designation:
Japanese get 10 "Off" days per month - gaijin get 8;
Japanese pilots are given their birthday as an "Off" day - gaijin are not;
Japanese get unlimited, paid Sick Leave - gaijin get 0;
Japanese pilots are issued with a flight bag foc - gaijin are told they can buy them for JPY10,000;
Gaijin must pay for lost uniform items - Nihonjin have them replaced free;
Japanese pilot discovers cracked fan blade on engine during walkaround,and is given an A&E award for his astute observation - gaijin pilots discovers Sys B hydraulic leak during walkaround (after being told "Ship is okay" by maintenance staff)...no recognition;
Gaijin male being spat at by Japanese male, because the gaijin was with a Nihonjin female;
There are many, many clubs (and some onsen) that bar gaijin entry..."Japanese only!".
The above are a few examples that I'm quickly able to pluck from the top of my head.
As JapJok has stated, the DIFFERENCE between Japan, and other developed, civilised countries, is that there is a recognition in the latter that all people have the right to be treated equally.
This is NOT the case in Japan - it is endemic in their culture, that even within their own, there is discrimination - the burakumin, the 3rd and 4th Japan born Koreans and Chinese who are still regarded as non-Japanese.