The article is devoted to the issue of repatriation of Ainu ancestral remains, collected by Japanese researchers in the second half of the 19th - 20th centuries. It is the most crucial current issue for many Ainu people who are trying to regain the language, the distinct culture, and identity. The article analyzes the positions of the Japanese Government, the Hokkaido Ainu Association and Ainu rights activist groups and movements. The article examines the contradictions that arose in Japanese society concerning the process of repatriation. Discussions in Japanese society during this problem were analyzed, and its significance for the Ainu communities is revealed. It was found that the discussions mainly arise in connection with the idea of transferring the remains to the memorial hall located in Symbolic Spaces for Ethnic Harmony, which was opened in July 2020. Research also showed that the problem under study is largely related to limitations in ethnic policy implementation and realization of indigenous peoples’ rights in Japan. In addition, the process of repatriation of Ainu ancestral remains is compounded by the lack of unity of the Ainu as a community. Therefore, reaching agreement between the government, the academic community, and critical Ainu rights activist groups proved extremely difficult. However, it was concluded that there is a potential to resolve the issue and consensus could be reached in the near future.