Autonomy and control disputes continue in public institutions, especially in the science and technology related public sector research institutes. The purpose of this study is to compare autonomy and control of the Korean Government-supported Research Institutes and the US National Laboratories, the model institution of the Korean GSRIs. Based on the extant research, the autonomy and control-related fields are divided into 'governance', 'ex ante control' and 'ex post control' in terms of 'to whom is the research institute responsible?' and 'how does the government ensure the responsibility of the research institute?', respectively. From the comparison of the two countries, it seems that it is difficult to view government control of research institutes in Korea as more severe than that of the US. Autonomy and control fields are influenced by national characteristics, and some institutionalization can be observed. In terms of governance, US national labs have been responsible towards a single ministry, but in the way they were responsible, market side was emphasized more, and ex post control was more prominent. In Korea, the responsibility of the GSRIS for the ministry was not clear due to the existence of the research council, but the hierarchical ex ante control was somewhat prominent with regard to securing responsibility. The results of the study show that it is necessary to increase the linkage with the ministry in order to secure the responsibilities of the GSRIs in Korea. Also, considering the characteristics of the research institutes, it is desirable to avoid appointment of the directors by the government or frequent restructuring of the GSRIs. The research results imply that in the planning process, it is necessary to expand the role of researchers. Moreover, in maintaining the appropriate level of autonomy and control, it is important to acknowledge the role of the PSRIs, to build a trusting relationship between the ministries and research institutes, and to form a culture of responsibility among researchers and institutes.