While history advanced in this way, collisions between history and nationalistic views of history occurred (for example, the incident of "Shinto is a remnant of the ancient custom of worshiping heaven," Nanbokucho-Seijunron (an argument on legitimacy of either Northern or Southern Dynasty) in the period of the Northern and Southern Courts (in Japan), and the incident of the emperor-as-organ theory).
こうした歴史学の発展の一方で、歴史学と国家主義的な歴史観との衝突も発生していた（「神道は祭天の古俗」事件、南北朝時代(日本)南北朝正閏論と後世への影響、天皇機関説事件など）。