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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