Membership in organized Christianity is certainly less than 1% of the Japanese population. Japanese culture has always had a looser structure to religions in general and the Tokugawa shogunate period with the whole "Kakure Kirishtan" subculture which hid Christian symbolism beneath Buddhist and Shinto concepts has made it all the more likely that organized forms of Christianity would be generally rare. They don't want a repeat of what happened to them after the Shogun took control where they were forced to perform a fumie on icons of Christian faith.