While this is annoying and is excessive to what's required in law (it must be done at least yearly, and most banks do not try to annoy foreign residents more than what's legally required), Japan does require all Japanese-domiciled bank that they verify that the owner is either a Japanese national or a long-term resident in Japan. In fact, most Asian countries do have a "must be a citizen or resident" or even the much more stricter "must be a resident" requirement.
At least it's not India, according to Mastercard and Visa India even prohibits foreign long-term residents from maintaining an account in their country of nationality (and therefore we must always certify that upon our knowledge we do not send cards, even debit, to India).