Safety management systems (SMS) are now being implemented throughout the aviation industry. This research was designed to investigate some of the organizational factors affecting the SMS performance in a military organization, specifically the Royal Malaysian Airforce (RMAF). The factors identified from existing organizational design literature were modeled and tested. The study population consisted of pilots and engineers from different air bases throughout the country. A survey was employed as the means of primary data collection using a cluster sampling techniques combined with secondary data obtained from published reports and statistical data from authorized agencies. The results indicate that Organizational Identity and Organizational Behaviour to have a significant impact on the RMAF Safety Management System performance with Safety Culture playing a significant mediating effect. The research findings will benefit towards improving the safety culture where organizational factors play an important role to the performance of SMS. Continuous improvement in flight safety will lead to a high-performance culture enabling the RMAF to perform its mandate more effectively.