Japan is the country with the lowest level of crime in the world. Assaults are infrequent and theft extremely rare.
During my first visit to Tokyo,somebody I had met in my youth hostel told me that he had left his wallet on a shelf in a shop the evening before. The next day, he went back to the shop and tried to explain to the shopkeeper, who did not speak a word of English, that he had left his wallet and he asked whether anyone by any chance had handed it in. He kept repeating the story to the shopkeeper, who obviously had no idea what he was saying, but he finally understood that the shopkeeper simply wanted to tell him that if he had left something somewhere there was no reason why it should not still be there. And indeed, there was the wallet still on the shelf and nobody had touched it.
So it is not a risky country, but it does no harm to use basic common sense (put valuables and travel documents in a safe place and keep an eye on your luggage).
Any risks in Japan are the natural risks of the region. As the Japanese archipelago is situated at the junction of 4 large tectonic plates, it is hardly surprising that from time to time there are low magnitude earth tremors.
If the risks of natural disasters (tsunamis, typhoons, violent earthquakes ) are always present (as was proven in 2011 with the accident in Fukushima), Japanese infrastructures have been built to cater for this. By keeping a close eye on the weather forecasts and a by following advice to avoid the coast when necessary, the risk is minimal.