Auditing plays an important role on having transparent financial statements especially in general organizations such as municipality, etc. A good implementation of auditing system helps reduce any possible fraud and increase the efficiencies of organizations. In this paper, we present an empirical survey to discuss barriers confronting auditing system. The proposed model designs and distributes a questionnaire between two groups of auditors and municipality managers. Cronbach alpha and KMO tests are used to verify the overall qualification of the survey and they are well above the minimum desirable level. The survey tests ten hypotheses including the effects of lack of standards and criteria, lack of experts, lack of awareness on advantages of auditing system, existence of conflicts in laws and regulation, etc. The results of t-test survey confirm all ten hypotheses and the implementation of Freedman test indicate that auditors have blamed using traditional methods as the most important barriers in using auditing techniques while managers believed lack of sufficient laws and regulations was the most important factors obstacle for using auditing system.