A major element of internal control in government is an independent and professional internal audit function. In most jurisdictions, government internal auditors continue to use traditional manual auditing method of testing controls by performing the tests on a retrospective and cyclical basis. Judging effectiveness of an internal control system through manual means is subjective. This can be minimized through use of the capabilities of a FMIS which most governments have implemented. Unfortunately, internal auditors have not been able to leverage the power of FMIS applications due to lack of awareness, skills and access. This paper discusses the role of internal auditors in the development of an FMIS application, using the system to conduct audit and leveraging the data available in FMIS. It introduces the reader to the usefulness of embedded controls, data analytics and computer aided audit tools, continuous online auditing and riskbased internal audit in relation to FMIS. This paper concludes that effective use of FMIS functionalities and data for internal audit needs is in its infancy. Proper advocacy, outreach and training can help internal auditors to gainfully use FMIS in their work enhancing effectiveness and efficiency of the internal audit function and making it relevant in the current environment, bringing benefits to the government and ultimately the citizens.