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The objective of this study is to analyze the problems and provide political implications concerning the management process of national R&D performance in South Korea. National R&D budget of the Korean government is continuously increasing. Thus, interest on performance of national R&D programs has been also increasing. Based on regulations related to the management of national R&D programs, institutes which exclusively manage the national R&D performance are formed. The institutes collaborate R&D performance through NTIS (National Science & Technology Information Service), a system which government officials, researchers, other users could freely access to. This study identifies the problems resulting from R&D performance management process and provides solutions based on investigations on current status of both performance information achieved by managing institutes, and NTIS, interviews with experts, statistical analysis, etc. The findings of this study could be applied as basic information in terms of decision making process for efficient management of national R&D performance.