Japan isn’t really in a good place from a natural hazard standpoint. Located on a major plate boundary, it is prone to major earthquakes. It is also in the crossroads of Typhoons as they start their northward turns, meaning they often sweep over or by the islands, dumping tremendous rain as they decay even if they do not make direct hits with high winds (which they do as well from time to time).
This map shows the damage swaths of natural disasters in Japan just in the last 72 hours:
Typhoon Jebi made landfall earlier this week, with at least $15 Billion in impacts, and causing additional deaths and in particular more flood damage on the top of catastrophic flooding earlier this year which is responsible for at least 300 fatalities. This summer also saw a deadly heat wave. And now there has been a 6.6 magnitude earthquake on the northern island of Hokkaido. Landslides (mudslides actually) are responsible for much of the damage and fatalities as the ground all across Japan is saturated.