Internal audit is one of the key activities used to control the implementation of government policies and programs. Yet, studies show there are various factors that can affect the quality of internal audit in its implementation. Based on this background, this study aims to examine the extent to which competency, independence, and professionalism of internal auditors and time budget pressure affect the quality of internal audit of the Ministry of Marine Affairs and Fisheries (MMAF). To observe causality between the factors and audit quality, this study applied qualitative approach through literature review and direct survey on the ministry’s internal auditors. Seventy people were taken as samples randomly and proportionally based on the auditors’ position. The results show that only competence and professionalism of the auditors that significantly affect audit quality, while other factors are indicated have less effect. Furthermore, this study found that reliable planning and quality control played a pivotal role in audit quality assurance. According to this research, it is necessary to increase the competence and professionalism of internal auditors to improve the audit quality. Government internal supervisory apparatus maintains independence and auditors maintain objectivity. In addition, this study also notes that the audit time calculations need to be done more thoroughly by the management.