Internal audit processes in regional government institutions often face challenges such as time inefficiency, low transparency, and poorly digitized documentation. This study aims to develop an E-Audit system to enhance the effectiveness of internal supervision in a regional inspectorate environment. Employing a user-centered design approach and a structured system development methodology, this research involved key roles—auditors, technical controllers, and follow-up teams—throughout the design and testing stages. The developed system integrates three core phases of the audit process—planning, reporting, and follow-up—into a single, modular, and interactive digital platform. Implementation results indicate a significant improvement in audit efficiency, with a reduction of more than 50% in process duration compared to manual methods. The system also enhances documentation consistency through digital audit trails, role-based dashboards, and automatic reporting features. User acceptance testing revealed a high level of satisfaction, with users highlighting the system’s ease of use, increased accuracy, and alignment with daily audit tasks. Additionally, user feedback emphasized the need for integrated notification features and inter-unit communication tools, indicating readiness for more advanced digital transformation. Overall, this study provides practical value as a model for digital audit implementation at the regional government level while contributing to the advancement of Computer Science through the application of software engineering principles and information systems to support digital government oversight. The developed E-Audit model can serve as a reference for designing real-time collaborative public auditing systems relevant to the development of information systems engineering and computational governance.