Abstract The aim of this paper is to elucidate the features of the policy-making mechanism of Japan's Council for Science and Technology (CST) focusing on the policy-making processes of comprehensive recommendations. The CST is the highest decision-making organization in Japan's science and technology administrative process and the recommendations have a great influence on the direction of national science and technology policy. The main results are as follows: In the CST, the organizations are never static but very flexible. The dynamic creation of deliberating groups occur in accordance with the development of the policy plan. Thereupon, the incessant negotiations between internal groups of the related ministries are very essential, and the policy-making process is achieved in this interactive way among the policy-makers in participating organizations. In this process, the dual-post holdings (DPH) in the vertical direction of the hierarchy can be seen frequently within the CST. This plays an important role in communication and is a very effective method of information transfer and consensus-building in policy formation requiring a high degree of expertise such as science and technology.