Anywhere in the world, noncitizens have fewer legal rights than citizens. Japan's Supreme Court would agree: On June 2, in a landmark case granting citizenship to Japanese children of unmarried Philippines mothers, judges ruled that Japanese citizenship is necessary "for the protection of basic human rights."
A shortage of rights for some humans is evident, however, whenever police partake in racial profiling — for example, stopping you for walking or cycling while "gaijin." Japanese citizens are protected against such random interrogations by the "Police Execution of Duties Act," which requires probable cause of a crime. But noncitizens, thanks to the Foreign Registry Law, can be questioned at anytime, anyplace, under penalty of arrest.
The societal damage caused by this is not so easily compartmentalized by nationality. Denying legal rights to some people will eventually affect everyone, especially since non-Japanese (NJ) are being used as a proving ground for embryonic public policy.