One should be aware that while Japan is generally safe, you can still get into trouble if you throw caution to the wind. Among the crimes that visitors have encountered - particularly around drinking / clubbing / nightlife areas - are bar scams and drink spiking. A typical bar scam can start with a new "friend" introducing you to a bar and ends with a demand for thousands of dollars for a few drinks, enforced by some intimidating thugs. Drink spiking can happen when someone buys you a drink or when you leave a drink unattended, and ends with you being robbed or worse.
If you're accustomed to high crime zones, your natural level of situational awareness will probably keep you out of trouble. If you're not so streetsmart, you should keep in mind that Japan, like any country, is not a crime-free paradise.