The biggest threat to travellers is Japan's general aura of safety. It's wise to keep up the same level of caution and common sense that you would back home.
The following government websites offer travel advisories and information on current hot spots.
Australian Department of Foreign Affairs (www.smartraveller.gov.au)
British Foreign Office (www.gov.uk/foreign-travel-advice)
US State Department (http://travel.state.gov/content/passports/english/country.html)