Recent historical investigation into the rise of ‘biopolitical modernity’ in China has shed some surprising light. While it was long thought that British public health initiatives entered China via Hong Kong, the recent work of Ruth Rogaski, Philippe Chemouilli and others has established that it was actually early Japanese colonialism that played the crucial role. It was the Meiji Empire's hygiene reform projects in Taiwan and Manchuria that provided the model for Republican China. Curiously overlooked by medical historians has been one of the major early works of Japanese public health that directly inspired and guided this colonial medical enterprise. This was that of the Japanese health reformer and colonial officer, Gotō Shinpei (1857–1929), and it was undertaken in Munich as a doctoral thesis under the supervision of Max von Pettenkofer. In this article, I focus on the way in which Shinpei dealt in his thesis with the relations between centralisation and local self-administration as one of the key issues facing hygienic modernisation and colonial biopolitical control.