Recently, information technology is considered as a basement of management for industries as well as administrations. Especially, government agencies deal with more high sensitive and Important data than other businesses, so, their security managements should be fair and efficient. At present, most government agencies possess and operate their own information security systems, but apply them for the sake of formality only, even do not adapt an audit system for management polices. This paper presents a design and implementation of an automated audit system which is suitable for the operation environment in government agencies, using the audit system based on the BS7799. The. proposed system aims to objectively, numerically and daily control the ISMS (Information Security Management System) for different level of government agencies. In addition, it permits to design and implement an adaptive audit tool, in order to meet a given condition of audit organization and guard the personal relationship between the auditor and its counterpart.