1. Travel with China. There was a huge amount of inter-country traffic up until the New Year. 2. Population density. Japan is quite high, and this should increase the country's R0. 3. Population demographics. Over 20% of Japan's population is over 60. This should increase the CFR for the country.
So there are two basic scenarios. One is that Japan is somehow mis-counting patients and deaths (similar to kodokushi). This could also be intentional, in a misguided attempt to protect the economy and the Olympics, or it could simply be a bureaucratic flaw in their methodology.
The second is that something unique to how the Japanese culture, healthcare system, etc is giving them an advantage.
Once we're on the other side of this pandemic, there's going to be a world of fascinating research/study into how different countries reacted to COVID-19, and how successful they were.