Originally Posted by
gengar
Private / introduction-only restaurants/bars/etc. aside, let's not pretend that there are not also many establishments in Japan that refuse service to foreigners, even if they are fluent in Japanese. It's rarer in central Tokyo, but in the Tokyo outskirts and even in central Osaka/Kyoto I've experienced it on many occasions.
OP - the extreme level of ingrained xenophobia is just something that you'll have to accept if you want to keep visiting Japan, unfortunately.
Had a strange experience at a Tokyo street market, when a vendor realized that the people I was with were Mainland Chinese (they often get mistaken for Koreans, and may well have some Korean in them, being from a place ~100 miles from the DPRK border).
The proverbial Japanese politeness evaporated instantly. I know that for historical reasons there isn't much love lost between these two nations but still it was very unsettling.