Naito and Kurakichi SHIRATORI had a heated dispute about the Yamatai-koku Kingdom; Naito's theory was that the Yamatai-koku had been established in the Kinai region (the five capital provinces surrounding the ancient capitals of Nara and Kyoto) while Shiratori thought that it had been in the Kyushu region.
邪馬台国論争については、白鳥庫吉の九州説に対して、畿内説を主張し、激しい論争を戦わせた。