Although science and technology collaborative networks (STCNs) have been studied and investigated for quite a while, the challenges of orchestrating these networks have received insignificant attention. In this paper, five collaborative networks in the field of strategic technologies laboratories, scientific laboratories, biotechnology, molecular medicine, and herbal medicine, established by the government agency in Iran in the years 2000-2018, were studied. In this paper, with systematic review of research, 41 challenges of the orchestrating formal collaborative networks of science and technology in Iran were identified at the level of network analysis. A researcher-made questionnaire was developed and distributed among the knowledgeable 5 selected collaborative networks, which were among the most active formal collaborative networks of science and technology in Iran. For analyzes, exploratory factor analysis and analysis of main factors and varimax rotation were used. Of the 41 indicators identified, 19 factor indexes were below 0. 5 and excluded from the analysis, and 22 indicators in the second stage and after the rotation were classified in 6 categories. According to the characteristics of the indicators in the classes, 6 titles were named for the classes: 1-membership (2 indicators), 2-network structure (6 indicators), 3-network position (3 indicators), 4-knowledge mobility (3 indicators), 5-appropriability (3 indicators) and 6-Stability (5 indicators). In the end, research limitations were also presented.