Operational audit plays an important role on managing governmental budget. It helps control government spending and other important budgetary issues. This paper presents an empirical study to find out the possible barriers on implementing operational audit. The proposed study distributes some questionnaires among supreme audit court of auditors and analyzes the questions. The results indicate that many governmental organizations are not strongly committed to rules and regulations. There are not sufficient standards on auditing programs and many governmental agencies do not even use operational budgeting system since they are not aware of the benefits of such system. There are some of the most important challenges of having operational budgeting and paper suggests some guidelines for having better regulation on removing the main barriers.