Due to the fragile institutional structure in developing countries, formation of national innovation system and continuing its development faced with some problems. One of the most efficient players in the innovation system, and then in NIS, are intermediary institutions that have some useful functions. These functions can be managed to reduce or eliminate these problems. The connection between the functions of these institutions and problems in our national innovation system is selected as the aim of this study.In this study, the problems of national innovation system are classified from a performance-oriented approach in 6 categories: policy making, facilitate and direct the activities of research and innovation, research and development, entrepreneurship, human resource development and technology diffusion. Then, in order to correlating the functions of intermediary institutions with their impact on problems in the national innovation system, the functions of intermediary institutions were classified in 4 categories: support and infrastructure, finance, mediatory communication and consultation.With the help of opinions of 35 experts through a questionnaire, the impact of each function of the intermediary institutions to overcome the weaknesses of the national innovation system was determined. Support functions had the most impact on facilitating and directing the activities of research and innovation; finance functions on research and development and entrepreneurship; mediatory functions on technology diffusion, and consultation functions on entrepreneurship and technology diffusion.