Public safety of Japan is one of the best in the world.
You rarely get your stuff stolen or face some dangerous situations.
In fact, no body will attempt to steal your stuff even if you are sleeping in the train.
Thus, you pretty much don’t need to do something special to keep yourself safe, however there are some regions that are risky to visit in Japan.
Kabuki Cho in Tokyo Shinjuku is an infamous town. Drug dealers, yakuza, and other rip off businesses exist there. If you step into this town in daytime, you won’t need to worry that much, but at night, this place could be very dangerous.
Recently, the public safety of this town is getting a lot better; however, I would not recommend you to go there.
Another famous one is Nishinari town.
This town is also known to be dangerous.
A lot of daytime workers work there and public safety is very bad.
Food in Japan is well controlled so you don’t need to worry about eating a raw fish, clams, and meats.
They are all kept clean and fresh.