IMHO, in Japan the "racism" tends to be more an institutionalized caution against most foreingers; common gaijin complaints such as trying to get a credit card or rent an apartment. It's partly to be expected when many gaijin have set a bad example by skipping country on their debts or turning their apartments into flophouses to save some Yen. But on a personal level the Japanese are quite hospitable and friendly, if you make the effort. Singapore was just the opposite: open to do business with foreigners but not so much be friendly.
Those were our general experiences, observations, and conclusions.
To answer, once and for all the title and question at hand: "Is Japan a Racist Society", the answer would be "maybe yes, maybe no. Maybe some Japanese make it that way, may some Japanese don't make it that way."