It has been believed that the high priest of the Higashi-Hongan-ji Temple received and buried Kondo's remains, but there is another theory that his comrades took the body back and buried it at Hozo-ji Temple in Okazaki City, Aichi Prefecture, and there is in fact a mound for Kondo's head at this temple.
近藤の遺体は東本願寺法主が受け取り埋葬したとされるが、一説に同志により奪還され、愛知県岡崎市の法蔵寺(岡崎市)に葬られたともいわれ、同寺に近藤の首塚がある。