As the Science of Science, Technology and Innovation Policy program is carried out in Japan, efforts to secure the integrity of evidence-based policy making are needed, along with the promotion of research, human resource development, and system building. In other words, it is necessary to ensure that stakeholders share a common understanding on the relations between science and government, and fulfill their respective roles and responsibilities. Meanwhile, recently in Japan, much discussion has been done on the relations between science and government in general. The Japanese government is now moving toward enhancing the systems for scientific advice, while the Japan Science and Technology Agency (JST)'s Center for Research and Development Strategy (CRDS) has issued in March 2012 the draft principles regarding the roles and responsibilities of science and government in policy making. This paper summarizes various discussions that have been made recently in Japan on the relations between science and government, including the content of the draft principles, and point out that, in promoting the Science of Science, Technology and Innovation Policy program, related efforts are necessary.