110 for police
119 for fire and ambulance

Japan is well known for being a safe country, but it is by no means a crime-free or
disaster-free country. It’s best to take the same precautions you would in your home country while also bearing in mind that—as a foreigner—you might stand out in your community. In the past there have incidents of JETs witnessing or being harassed, burglarized, stalked, or attacked. Please contact your PAs, supervisor, or CLAIR immediately if you experience an incident or you feel that your safety is being threatened.
Make sure your print out this list of Emergency Japanese phrases and put it somewhere accessible in case of an emergency!

Check out these other sites with great information on what to do in emergencies in Japan:

The Expat’s Guide to Japan: Emergencies

Savvy Tokyo: Easy Japanese for Emergencies and Calling Emergency Services