One part of it is that the Japanese police won't arrest someone unless they think they can nail them. A lot of murders may be ruled suicide because there's no convenient scapegoat, he-said-she-said rape cases not pursued, etc.
OK, but that's approximately true of criminal justice in the US. For instance: wiretaps are administratively expensive to pursue, and so police don't request them until they're sure they've got enough evidence to win the warrant. But civilians aren't persuaded by this logic; instead, they see it as evidence that the whole system is tilted in favor of the police.
It should be as disquieting (or not disquieting) in Japan as it is in the US.
If you look at the criminal justice system as having some amount of diagnostic sensitivity at each stage in the process (having both false positives and false negatives as all systems do), then our comparatively lower conviction rate means that (assuming end-of-the-day-justice is equal), we should be even more willing to waste people's time developing cases that have no merit (because more of the diagnostic sensitivity is in the trial/conviction stage). So it's not unreasonable to assume it's easier to get a wiretap in the US than it is in Japan -- another explanation is that Japan is substantially more likely to have false negatives (as implied elsewhere -- but the false negative rate for many crimes in the US is quite high, as roughly half of all murders go unsolved). Could also be that the diagnostic sensitivity is extremely bumpy in America or Japan (read: basically one or two steps / people get an extremely high share of the criminal justice discretion).
