Japan is fairly safe in certain ways - you’re not at risk of getting shot like in the US, sure.
But the police and justice system is very dysfunctional, with crime statistics being under reported, and many murder cases being tossed aside as “suicides” or “heart attacks”.
Even without taking this into account, crime rates in Japan are comparable to those of safe European countries.
And this is not even touching the HUGE pervasive problem that Japan has with sexual assault. If you’re a woman living in Tokyo, you most likely have been sexually assaulted in your life, likely more than once, and likely by a coworker or in public transportation.
Japan is great in certain ways, and still very backwards in many others. But it is not some magical country where there is magically no crime and people are the most honest in the world because of some mysterious Japan only gene. On many metrics, Japan is aligned with the most developed Western European countries (including the famously quoted “fertility rate”, which is actually the same as Austria or Germany). If anything, it is the US that is an anomaly in many ways (crime rate, financial inequality, drug use, etc).