Japan is a first world nation with stringent health policies and practices. As such, there are no required vaccinations nor vaccine recommendations for travel or residence in Japan. There is no malaria risk within the nation and thus no preventative measures need to be taken.
Those that are allergic to pollen from cedar or cypress trees should stock up on appropriate medication as the spring months can be particularly difficult for those that are allergic. Some popular prescription antihistamines are available in Japan, but many expats choose to acquire their medication at home where the dosage is often stronger.