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.
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