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The purpose of this study is to investigate the sector-by-sector governance of Japan for support of transdisciplinary study, focusing on the cases of government sector, for-profit sector, and non-profit private sector. The research method of case study is applied to an example of the government sector, the Japan Society for the Promotion of Science’s ‘World Premier International Research Center Initiative (WPI)’, the ‘Beyond AI Institute’ by SoftBank Group Corp. as an example of the for-profit sector, along with the support of a research project by the Foundation for the Fusion of Science and Technology as an example of the non-profit private sector. Then these cases were analyzed particularly in terms of coherence, flexibility, and intensity. Using forms such as consortiums, which are irrespective of the existent university ranks, the advancement of support system for the commercialization of corporate-laboratory links and securing diversity of targets for convergence support and integrated management, it was concluded that the coherence, intensity, and flexibility of governance in support of transdisciplinary study could be increased as a result.