Purpose The purpose of this study is to compare and analyze the efficiency of R&D projects depending on their managing institutions. Methods In this study, the quantitative and qualitative efficiency of scientific and technological performance of ‘SW Computing Industry Source Technology Development Projects’ from 2009 to 2018 were analyzed using Data Envelopment Analysis(DEA) techniques. Results IITP(Institute of Information & communications Technology Planning & evaluation) showed better scientific efficiency than KEIT(Korea Evaluation Institute of Industrial Technology) in terms of quantitative and qualitative efficiency. In contrast, KEIT management task showed better technological performance, in particular qualitative efficiency, than IITP. The results indicate that the difference in managing institutions can make a difference in terms of R&D performance. Conclusion This study is meaningful in that it confirmed that there are differences in national R&D efficiency depending on the management institution, and it can provide guidelines for R&D project management policies.