Arrested is not the same as convicted. I lived in Japan for a few years, and I have heard of similar situations to what the article describes.

In Japan you can be arrested while an investigation is in process, only afterwards you will be indicted. Additionally, Japan does not permit defendants to post bail prior to an indictment.

Yes Japan has a really high conviction rate, but that is because they indict only cases were a conviction is likely.

Arrests don't need to lead to the person being indicted.