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Existing studies on performance analysis of R&D funding have focused only on the object of measurement, and have not considered potential relations among various influential factors. In this paper, we developed performance indices to investigate further at individual company level. Empirical analysis was performed using the performance survey data for the science and technology promotion fund in Korea. The results of performance analysis could be used to provide the individual companies with insightful feedback information for improving their productivity. We hope this study contribute to better management of national R&D funding.