Health
Medical services in Japan are of high quality (at least in cities) and are widely available, although expensive. Drugs are available, but travelers need to carry their prescriptions and know the generic name of the medication they take, as it can be sold in Japan under a different name. Also, some prescription drugs are not allowed to be brought into Japan (like narcotics, psychotropic drugs, stimulants and codeine). Travelers should also be aware that most doctors don't speak English, with the exception of some main hospitals in major cities. Japan National Tourist Organization (JNTO) can provide a list of English - speaking doctors and dentists as well as hospital where medial staff can communicate in English.
Proper travel medical insurance is highly recommended since the cost of treatment in hospitals is very high.
Hospital end doctors will usually require full payment at the time of treatment or proof that the insurance company will pay for the service.
Currently Japan doesn't require any immunizations or health certificates on entry.
Tap water is generally safe to drink throughout Japan. Food is also safe to consume. Hygiene standards are high.
It is recommended to avoid walking barefoot in any stagnant water or on rice fields as there could be a danger of contracting parasites.
Safety
Statistically, Japan is one of the safest places in the world, with crime rates much lower than many Western countries.
Street crimes are uncommon, so is pickpocketing, but travelers should also use common sense in protecting their valuables, particularly in airports and on the crowded rail network in Tokyo.
If you loose anything valuable, it is worth inquiring if it's been found. Travelers can report lost or stolen things at police stations or police booths (kobans) that are commonly found by the streets. Japanese often return found valuables to police or "lost-and-found" offices, so there is a chance you receive your things back.
The police emergency phone number is 110. Medical and fire emergency number is 119. There is also a police emergency help line for tourists (in English) in Tokyo: 03-3501-0110 (Mon-Fri, 8:30 am - 5:15 pm).