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Japan is one of the safest countries in the world, and while at times many Japanese do not speak English, most people are extremely hospitable and will go out of their way to help travellers find their way around, and make the most out of their trip to Japan.
The actual crime rate is very low in Japan, and is not something that should concern travellers to the country. Of course common sense should be applied anywhere in the world, but it is rare for travellers to feel anything but safe in this beautiful country.
As for those bugs and pests that are a little harder to spot, then rest assured that no inoculations are needed to enter Japan from anywhere in the world.
The tap water is safe to drink anywhere in Japan, but bottled water and mineral water are also readily available.
If something unforeseen does happen to you on your trip, the hospitals and medical facilities are among the best in the world, but we always recommend you to make sure your travel insurance is valid and appropriate.