Surely the Yamato people are indigenous to southern Honshu. And surely the Ainu are indigenous to Hokkaido. Certainly the Ainu are not not indigenous to Japan.

"Indigenous" is frequently used in a context where a people's rights to their ancestral lands are threatened. It is an assertion of their claim to places where they are threatened. In the case of the Ainu, much of Japanese colonization and colonialism was justified with the ideology that the Ainu were "dying race" or "disappearing". This was acompanied by the usual policies of social oppression and linguicide—taking them away from their parents to Japanese-only schools and beating or shaming them if they dared to speak the language of their parents.