The police can also keep you in jail for months without charging you with anything. This pretty much ends your career and family life.
All of the above has happened to e.g. tourists accused of stealing a single dumpling.
Forced confessions are the bulk of what makes up that 99% conviction rate. Japanese lawyers always advise their clients to produce a confession regardless of the circumstances.
Non-natives are strongly advised to follow the law to the very letter and that they're fucked if ever arrested no matter how insignificant the infringement might first appear - and police will downplay the severity of infringement to make you confess.
The Japanese criminal justice system is only marginally better than Chinese. It's one of the areas where they just failed to advance as a society.