The concept of evaluation plays a critical role in recognition of the existing situation and finding out the extent to which the objectives of organizations have been achieved and as a result, improving the organizational efficiency.Moreover the performance evaluation is an outstanding element which provides the grounds for improving the existing processes and promoting the organization's profile by highlighting the improvable areas as well as the potential threats and strong and weak points.Following the approval of the "Regulation of Administrative Organizations Performance Evaluation" by the Cabinet and the establishment of an evaluation system in all the administrative departments and foundations across the nation. The Ministry of Science, Research and Technology also developed and established its macro-level performance evaluation system for both administrative and academic sections during the academic years of 2001-02 and 2003-04.After reviewing the related literature both inside and outside the country, a list of potential evaluation factors and indicators was prepared. Further, the Modified Analytic Hierarchy process was used to determine the weights of the factors and indicators were identified. The shortlist consisted of 6 factors and 11 indicators for the academic section and 7 factors and 23 indicators for the administrative section. Following the design, production and distribution of the questionnaire, the target data were collected to be analyzed for the changes during 3 academic years based on the 'descriptive statistics method'.The research outcomes show that most of the evaluation indicators, for both administrative and academic sections, were on a growing trend; and while a number of indicators appeared declining, the overall path could be titled as satisfactory with regard to the Ministry's policies.