This paper reports the initial findings from a large scale survey of Japanese researchers on the knowledge creation process in science. The survey was jointly conducted by the Institute of Innovation Research of Hitotsubashi University and the National Institute of Science and Technology Policy . It collected 2,100 responses on research projects, one third of the sample are from highly cited papers (top 1% in the world, H papers hereafter) in each science field by year and the rest of are from the other randomly selected papers (N papers hereafter). We call the research projects that yielded H (N) papers by H (N) projects. The survey covered all scientific fields, including social sciences, and characterized the motivations of the research projects, the knowledge sources which inspired the projects, uncertainty in the knowledge creation process, research competition, composition of the research team, sources of research money, and the research outputs, including the papers, the patents, the collaborative research projects.