I'm interested in how one might go about getting vaccinations for Japanese encephalitis and antimalarial drugs while living in Japan. I have no idea how easy/difficult it is to access these things within the Japanese health care system. Help please?

I dont think there are vaccines for japanese encephalitis, you just have to be careful when you go outdoors so you dont contract JE via mosquitoes. Wearing long sleeves or spraying mosquito repellants are wise actions. In terms of malaria, there are drugs and vaccines nowsdays.

I would have said the opposite. I don't know how you go about getting it in japan but there is definitely a vaccine for Japanese Encephalitis. A vaccine for malaria??? If you know of one that definitely works I want to buy shares in that company. There are still millions of deaths every year from malaria...
Most people stick with using prophylaxis such as doxycyline or others but if it's for Japan I doubt you would need it.