As it has been explained many times before, the reason why the criminal conviction rate is so high in Japan (99.3%) is for the exact same reason why the federal criminal conviction rate is so high in the USA (99.8%). The state will prosecute you ONLY IF they are sure to win.
The reality on the ground is that in a looooot of cases, the state simply does not prosecute the criminal because they are not absolutely sure to win.
Here in Japan you can get assaulted by a dude, know him personally, have injuries and stuff, but if the police cannot get an outright confession signed by the guy or a 4k120fps video footage, they will not prosecute him because they are not absolutely sure to win. They will tell you to fuck off and file a civil suit if you want justice.
Which is absolutely infuriating to those that have to deal with the justice system. Even in cases of murder, rape, or other outrageous things where the culprit is obvious, known by all including the police, if they are afraid of breaking the streak that their police district has for prosecution (the prosecuting chief really want to brag to the prefecture governor about his 100 consecutive convictions), they will drop the charges if they cannot bully the criminal into confessing, and you, as the victim, will have to spend years and tons of money in lawyer and court fees to civilly sue someone.