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Currently SMEs have been accepted as the main engine for establishment of electronic government structure based on innovation systems. This paper discusses this concept in developing countries and also the necessity to shift from SME,s orientation method to universities orientation method in developing countries as a paradigm of domestic management of e-government .So the study analyzes the innovation policy in universities based on a review of development program in an e-government structure. In an indirect process for determining the eligibility of higher education institutions to participate and create policy innovations in state e-government programs it has directed that institutions are eligible for participation if they meet two fundamental conditions: 1-Be able to evaluate ,monitor, analyze and predict fundamental changes in science and technology in order to keep abreast of the global fundamental changes in science and technology. 2-Be able to develop priorities plan to organize technological activities of the country to reengineer nationwide development of science and technology and to provide a This issues and circumstances are surrounding the initial development of evaluation and monitoring and major changes in procedure and standards. Also attention is given to some of the challenges that presently are posing for evaluation procedures as growing complexity, globalization and advances in instructional uses of electronic technology allow new forms of higher education provision to emerge. The exiting policies need to be re-examined, and new policies developed. While higher education innovations must be recognized, it is also true that monitoring agencies have greatly assisted their career. In this process monitoring agencies serve as a public brain system to advocate changes that will improve higher education practice.