The conviction rate is high because prosecutors have discretion over which cases to take to court, and there is no jury. The outcome of a bench trial is often predictable, and prosecutors will only take to trial cases they believe will succeed.

A large proportion of prosecutions in Japan rely on confessions, often obtained by duress. Even if only a small number of perpetrators (or innocent suspects) confess, taking only those cases to trail keeps the conviction rate high. The rate at which crimes are solved is somewhat lower -- less than 30% according to the article.