This study aimed at identifying and analyzing issues and challenges on the agricultural research and technology development under the national innovation framework. The survey consisted of two groups: agricultural researchers of Agriculture-Research and Education Organization and all faculty members of public agricultural faculties of Ministry of Scientific, Research and Technology. Using Cochran sampling formula and multi-stage sampling method, 188 researchers and 205 faculty members were selected in order to fill in the survey questionnaire. Using the SPSS, collected data analyzed based on explanatory factor analysis. Totally, factor analysis of three sets of issues and challenges on the agricultural research and technology development under the national innovation framework led to extract 13 factors, including agricultural structure and policy, infrastructure and resources of agricultural development, supportive services for agricultural development (level of agricultural development), investment and capacity building in research and technology, management of research and technology development, research and technology productivity, research culture, networks for research and technology development (level of national innovation system), agricultural research policy, impacts and effectiveness of agricultural research and technology development, integrated management of research and technology, institutional development for agricultural research and technology and systematic synergy of agricultural research and higher education (level of agricultural innovation system). Totally, these three sets of factors explained 64%, 75% and 73% of the total variances. Finally, using conceptual clustering for the extracted factors, a conceptual model of issues and challenges of agricultural research and technology development under the national innovation framework was presented.