I dunno. That suggests that it's not culture and it's not geography... So what's left? Genetics and history? I'd pick history, the accumulation of aggregate choices.
I don't understand the premise, where Japan is supposedly uniquely high-integrity. It ranks around the United States in metrics of corruption, sometimes higher and sometimes lower over the last 20 years, and historically was significantly worse than it is now. It's about as corrupt as any of the many countries on this planet that have the rule of law.