According to empirical evidence and noted implications of sustainable agricultural development as a systemic and multi-actor process, integration of the research function of higher agricultural education in Iranian agricultural research systems seems to be an ongoing and considerable necessity. With the aim of identification and analysis of institutional orientations, strengthening mechanisms and problematic challenges of university agricultural research in the agricultural research system of Iran, this explanatory research was carried out based on survey strategy. The population of this research consisted of all faculty members of public agricultural faculties and colleges of the Ministry of Science, Research and Technology (MSRT). Using a multi-phase sampling method, 183 faculty members were selected in order to participate in the research by completing the questionnaires used as a research tool. Collected data were analyzed using the Statistical Package for the Social Sciences (SPSS). Based on the calculated coefficients of variation, two groups of institutional orientations (structural/institutional arrangement and functional targeting) were ranked separately. According to the results of analyzing the strengthening mechanisms, five components were extracted, which explained 75.02% of the total variance. The explanatory factor analysis of problematic challenges extracted four principal components, which explained 75.026% variances of the analyzed set of problematic challenge items. Based on the percentage of variance explained by each of the factors extracted from the factor analysis results, a force field analysis is used to investigate the interaction of two opposing sets of forces, both driving and restraining forces of an agricultural research system that influence any change in the current situation. (Contains 4 figures and 5 tables.)