You are confusing several things. Japan has a low VIOLENT crime rate. Homicides, rapes, assaults, and such are among the lowest rate in the world. But burglary, theft, prostitution, illegal gambling, petty larceny while not high in Japan, it is not low either.
A "rate" means how many per X number of people. In regards to statistics dealing with population, the usual number is how many per 100,000 people.
As for "reported crimes", this is actually a good thing because it means people are more law abiding and trust the police so they report more crimes and therefore the authorities can catch and prosecute more criminals.
This means having low reported crimes does not make the place safer, but the opposite. In some of the worst crime ridden countries in the world, the people do not even bother to report it because nothing gets done because they have no confidence in the police and justice system due to it being incompetent and/or corrupt.