A couple of things.
While the _conviction_ rate is very high, the _indictment_ rate is somewhat low. Japanese prosecutors generally only pursue cases that they are certain they can win, and when you do that your stats are going to be artificially high. It is like if an NFL team only played exhibition games against low-division colleges – they’d have a near 100% win rate, but that wouldn’t be all that impressive once you know the details.
Beyond that, the Japanese criminal justice system is routinely criticized for its harsh treatment of people pending trial. Being denied bail is common, as is harsh treatment in order to obtain confessions and the inability to see friends or family. It is nicknamed _hitojichi-shiho_, or “hostage justice system”, by many. This results in many innocent people confessing to crimes simply to get out of the harsh treatment pre-trial.
Japan also doesn’t have as robust a discovery process as the US does. Prosecutors only disclose the evidence they plan to present in court – which will _obviously_ point to the defendant’s guilt – and are not obligated to disclose to the defense any evidence they have that might indicate innocence. This makes it much harder for the defense to present a case that the defendant is not guilty.
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