The destruction of Japan's cyclotrons by Occupation Forces after the Pacific War resulted in a major setback for experimental physics in that country. Key figures such as Yoshio Nishina, Sin-itirôô Tomonaga, and Ryôôkichi Sagane strived to help Japan rebuild its scientific infrastructure and regain some of its former eminence in the field, but in the wake of the dropping of the atomic bombs on Hiroshima and Nagasaki, the atom had new meaning. Local residents objected to the establishment of the Institute for Nuclear Study in Tanashi, Tokyo. Despite their protests, construction went ahead and the Institute of Nuclear Study (INS) opened in 1955. Within a few years, physicists sought to establish a second major accelerator facility. Sectionalism among physicists and shortage of funds plagued attempts to establish the National Laboratory for High Energy Physics (KEK) which eventually came into being in 1970. This paper reveals some of the problems that physicists faced and how they sought to overcome them within the context of a defeated Japan, wary of military research, and desperately seeking to rebuild its economy. Physicists sought to influence the direction of science policy and to deal with the concerns of citizens in a newly democratic Japan.