Alex posted a comment in Lessig's blog that since Japan has an over 90% conviction rate, it didn't matter that you are guilty until proven innocent. ToastyKen else said it was because the government prosecutes only when they know they are right. Both have some truth. The problem is that judges are reviewed by the bureaucrats and their careers depend on not rocking the boat. It is NOT an independent judiciary.
I found an interesting paper about this. Too bad I can't download the whole thing.
Ramseyer & RasmusenWhy Is the Japanese Conviction Rate So High?
J. Mark Ramseyer (Harvard Law School)
Eric Rasmusen (Indiana University)
Conviction rates in Japan exceed 99 percent -- why? On the one hand, because Japanese prosecutors are badly understaffed they may prosecute only their strongest cases and present judges only with the most obviously guilty defendants. On the other, because Japanese judges can be reassigned by the administrative office of the courts if they rule in ways the office does not like, judges may face biased career incentives to convict. Using data on the careers and opinions of 321 Japanese judges, we conclude that judges who acquit do indeed have worse careers following the acquittal. On closer examination, though, we find that the punished judges are not judges who acquitted on the ground that the prosecutors charged the wrong person. Rather, they are the judges who acquitted for reasons of statutory or constitutional interpretation, often in politically charged cases. Thus, the apparent punishment of acquitting judges seems unrelated to any pro-conviction bias at the judicial administrative offices, and the high conviction rates probably reflect low prosecutorial budgets instead.