This paper is devoted to the problems of studying and perception of the Japanese military intervention in the Far East and Siberia regions during the Russian Civil War in modern historical literature. The work discusses the relationship of the development of historiography of Russo-Japanese relations with public perceptions and targeted propaganda by political elites and authorities. Due to the peculiarities of Russia's geopolitical position, all the problems of international relations in the Far East region were considered through the lens of the country's territorial integrity. During the Civil War, the Bolsheviks successfully used anti-Japanese phobias to fight political opponents. The political propaganda attitudes formed in the Civil War and subsequent events of the Soviet-Japanese confrontation in the 1930s were transferred to the works on the history of Japanese military intervention. During the Soviet period, rather than studying the events and problems, historians focused on interpreting the official statements and the positions of the party and Soviet leaders. This trend is generally preserved in the post-Soviet historical studies too. The paper details the works of Russian historians and Japanese scholars over the past three years. A number of interesting studies are noted, for example, the works by the Japanese studies scholar K.O. Sarkisov, historians A.G. Teplyakov, F.A. Popov and others. In general, due to the lack of public demand and the inaccessibility of the documents, Russian historians do not tackle the topic even despite there being the occasion of the centenary of the events. The current level of studies of the history of Japanese military intervention in Russia remains at the level reached back in the 1930s. This situation reflects both the problems of Russian historical science and the current situation in Russo-Japanese relations.