Malaria may be found in a few coastal areas in the north but it is not a significant problem. If you require prescription medications, then make sure you have enough to cover the duration of your stay; as pharmacies will only fill prescriptions by Japanese doctors.
General hygiene is very high as the Japanese are meticulous about cleanliness. Food hygiene standards are also high but raw seafood carries an additional risk of parasitic infection and toxins. Visitors are often surprised that the toilets don't usually have soap or hand dryers. The locals often carry a small hand towel with them at all times. Another good option is to carry a packet of disposable wet wipes.
