I wrote my BA thesis on Japans human experimentation in WWII, so I can tell you a bit about that part. Before the war Japanese believed that their country is too small to provide for their growing population, so the logical solution was expanding their territories in order to gain new raw materials. In order to do that, they needed a strong army, so they started focusing their efforts on curing epidemics that affected soldiers and find ways to cure them. In the first decades of the 20th century preventing epidemics among soldiers remained the main goal in the scientific community. But new ideas emerged, ideas how to turn bacteria and gases into weapons to further their cause. The man behind these ideas was Shiro Ishii. For that he needed live test subjects and animal experimentation would not give him “viable” results. He needed humans and Japans occupation of Manchuria gave him and the scientific community just that. They built special labs where they experimented on humans. So in that aspect and in scientific field it wasn’t about “scientific racism” so to speak, but about providing new ways of battle in the form of biological warfare. It was not about eugenics or creating superior human race. They did think of Manchurian people (and Chinese and Korean prisoners in these labs) as an inferior race to their own, and so they were “suitable” candidates for experimenting upon. To conclude there was the belief that these prisoners were inferior, they did mainly view them as valuable, but expandable test subjects and not people.
Harris, Sheldon H. Factories of Death. Japanese Biological Warfare, 1932–1945, and the American Cover-up. Revised edition. New York/London: Routledge, 2002.
Gold, Hal. Unit 731. Testimony. China: Tuttle Publishing, 1996.
The Japanese Empire did employ “scientific racism” as a means to dehumanise other ethnic groups in Asia: this was intended to provide an ideological underpinning for Japanese expansion and to justify its colonial ambitions. From the late 19th century, a new field of ethnography emerged in Japan focusing on the relationship between the Japanese and other Asian groups; typically, this tended to portray the Japanese race as superior, and argued that Japan should become a ‘custodian’ of the ‘lesser races.’ To take one example, we can look at the Japanese colonisation of Taiwan: in 1873, an expedition was launched to the island, and Japanese rule was formalised with the Treaty of Shimonseki after the First Sino-Japanese War of 1895. Japanese ethnographers focused on the ‘savagery’ of the Taiwanese Aborigines: they were typically portrayed as primitive headhunters, in need of a ‘civilising influence’ (in this case, that of Japanese rule of the island).
Though the ‘scientific racism’ of Japan might seem to parallel that of Nazi Germany, there a number of important distinctions. Firstly, it seems the idea of ‘racial superiority’ was less integral to the ideology of Imperial Japan than it was in Nazi Germany. Secondly, the rhetoric of ‘scientific racism’ did not necessarily imply inherent ‘superiority’, but that of ‘racial seniority’ - that is, the Japanese portrayed themselves as more developed than their neighbours, such as the Koreans and Chinese, and tried to present their role as one of ‘guardianship’ in official propaganda. For example, some ethnographers claimed the Koreans and Japanese shared common descent: in this regard, the annexation of Korea could be spun as ‘reunification’ rather than conquest.
Sources:
E. Taylor Atkins, Primitive Selves: Korea in the Japanese Colonial Gaze (2010).
Robert Tiernay, Tropics of Savagery: The Culture of Japanese Empire in Comparative Frame (2010).
Whether it was the motivating factor or not, up until the end of WWII the Japanese Empire held an ideology of extreme racial supremacism, partially adopted from Western scientific racism and partially from Eastern ideas. Since the creation of the Empire of Japan and the rise of Japanese nationalism, a belief developed that the Japanese race (or Yamato) were the purest in the world and (according to Shinto myth) ultimately descended from the sun goddess Amaterasu and therefore divine. This was combined with Western eugenics and later Nazi racial ideology to argue that the Japanese were superior to all other races.
External propaganda, however, espoused Pan-Asianism, promoting solidarity among Asians against Western imperialism. Thus Japanese expansionism was justified as saving Asians from the West, as seen in how the Japanese referred to their empire during WWII as the "Greater East Asia Co-Prosperity Sphere." The imperialist and supremacist intentions were blatant in domestic propaganda, though, as demonstrated in the popular motto "hakko ichiu" (meaning something to effect of "the whole world under one roof").
The influence of Nazism is made clearest in the report "An Investigation of Global Policy with the Yamato Race as Nucleus," which makes explicit reference to Nazi ideology and slogans such as "Blood and Soil" and the concept of making "living space" for the Japanese people. However, the Japanese seem to have preferred the concept of "minzaku" (meaning something like "community") to the German concept of race, and maintained that other Asians could assimilate to become part of it. Patriarchal Confucian ideology was also utilised; the Yamato race playing the role of the father with the other Asian races as its children, emphasising putting everyone in their "proper place."
Effectively, Japanese imperialism and all the war crimes that came with it were justified by a combination of scientific racism, Eastern philosophy, mythology and political ideology.