There are a lot of things about Japanese society that many Westerners would find intolerable. Japan, for instance, ranks pretty much last on the list of industrialised countries for sex/gender equality, and is at least 20 years behind the US and EU in recognition of LGBT rights.

Japan doesn't have lower levels of violent crime than other nations because Japanese people are less violent, but because Japanese culture is very homogenous and socially restrictive.

The social consequences of criminal activity are severe, and the system of criminal justice is not very well regulated. People are often detained for lengths of time without protection of their rights in ways that would never be tolerated in the US or EU.