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In recent years, national R&D programs tend to become larger and more complicated, which necessitates strengthening the overall coordination of national R&D programs at the inter-ministerial level from the program planning stage. This paper looks into the status and problems of Korea's national R&D programs and proffers ways to improve the current system. It highlights the problems shown in the process of the 2004 overall coordination and their rectification:First, various ad-hoc private-led committees brought about inefficiency in decision making process. Therefore, it is necessary to streamline such committees and strengthen the function of the Office of Science and Technology Innovation. Second, in view of the implementation of the overall coordination system, it is necessary to identify the problems in full detail that were raised in the course of the previous year's overall coordination so that new projects can be allotted minimal grades and follow-up activities can be efficiently put into execution. Third, it is necessary to establish standing committees for constant review and efficient utilization that will be devoted to reviewing programs overlapped and their linkage. Fourth, priority of investment regarding the nation's strategic policy direction should be reflected. Fifth, given the lack of performance-based evaluation system, it is necessary to develop macro and micro evaluation indices in conjunction with enacting the tentatively named "Performance-based Law." The overall coordination system of national R&D programs should be supplemented and further developed in relation to the aforementioned problems and their rectification in order to enhance the expertise, fairness, and efficiency of the nation's R&D coordination system.