Getting denied because of medical conditions?

I've been thinking about applying to a doctorate degree course in a certain Japanese research instituion after completing my master's degree. But I have been quite afraid that I might be rejected from applying for a visa or possibly residency after completing the course.

I am suffering from some mental disorders and I have been wondering whether at any point (be that applying for students/research visa or applying for a residency later on) they can use my medical record as a reason for denying my application.