Nitpick: you mean conviction rate. 99.8% of people who are prosecuted are convicted.
This phenomenon is debated, but there are two generally accepted answers. The first is what you mentioned. Japanese prosecutors are much more hesitant to prosecute a case they might lose than other countries’ prosecutors. Your belief isn’t right, plenty of prosecutors bring a case against someone even if they aren’t 100% sure that they will win.
The second reason is that the Japanese criminal justice system is extremely harsh towards defendants. Evidence can easily be excluded from discovery, making it hard to prepare a defense. Defendants are often presumed guilty until proven innocence. Defendants don’t have a right to silence, they can often be forced to speak against themselves. Sound bad? It is.
Because they will never prosecute anyone they don’t think they will absolutely be able to convict. If they fail to convict, it would ruin their stats, so they only do it when they’re 100% sure. Unfortunately, that means if they’re not 100% sure they are able to convict, they won’t prosecute even if it’s 100% certain you’re guilty.
There’s also the “small” problem of courts there being very biased towards defendants. I mean, if you’re there, you must have done SOMETHING, right? Sadly, they have a mentality of “If something bad happened to you, you must have deserved it”. Sucks.
Part of it is an effect of crime rates in Japan being so low. There just aren’t a lot of serious crimes in Japan. So prosecutors are mostly bringing lower level, lower stakes cases and the authorities can devote enough resources to any major case.
Another effect of this is that there’s essentially no popular sympathy for a criminal lifestyle. Police can hold suspects without charge for weeks on minimal evidence, bail is rare, and there’s a social presumption of guilt for even getting caught up in this.
Goodhart’s law. Since the metric by which they judge their legal system’s efficacy is convictions, they strive to get as many as possible. This means they often do not even bother prosecuting cases they’re not confident will result in prosecution and pressure for a settlement instead. It also means that a lot of the time innocents are sentenced because if you find yourself in a court room you’re pretty much only coming out with a sentence. How you ended up there is of no concern.
Other factors are also at play. The Judicial System, due to societal and cultural factors, likes to present an image of a unified front, and that everyone is in agreement. They believe that disagreements will give off the idea that the organisation is fractured and at odds with each other. This is antithetical to the core concept of a trial, where the main activity is arguing. There is also the aspect of seniority, which is very important in Japanese society. The societal pressure is immense, and something like a judge, in a panel of judges, disagreeing with a more senior judge, is essentially career suicide.
Ultimately it’s a very intricate subject and I’m only scratching the surface.
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