Those claiming Japan is a racially pure society... Uhhh... not according to the Japanese. They don't even consider most Japanese, truly, racially Japanese. For example, look up the treatment of Okinawans during WWII.
Or, for another example, Koreans are, ethnically, the progenitors of the Japanese people. You will not find a more oppressed group in the industrialized world, though, than Japanese born Koreans.
Crime rates are as much perceptual as anything else. Since the rather... uhhh... violent end to WWII the Japanese don't see themselves as a violent people (though they still do have a violent mindset towards many things). They're a people that are fanatic, even fetishistic about violence; one just need look at their video games, or films (J-horror, body horror, Yakuza films, Samurai films, etc.) to understand that.
But they don't carry out those desires in near the rates Americans do. Mainly because the access isn't there.
That doesn't mean it's a perfect society, far from it. Murder rates could actually be much higher, but they tend to count the all too common family suicide as individual suicides, even when there is definitive evidence that a parent(s) killed their child(ren) against their will.