The establishment of IA function is important as an essential internal assurance mechanism in public financial controls and as tool for monitoring and evaluating financial management activities in government agencies.This study investigates the factors that contribute to the effectiveness of internal audit in Malaysian public sector. It is to determine the auditors perception toward the effectiveness of internal audit work, influenced by the quality of audit work in order to perform in effective manner as control instrument in public financial management. It also aims to determine the relationship between the effectiveness of IA and integrity of public management. The scope of study covers the internal auditors that working in the ministeries in Putrajaya. This study employs a cross sectional survey to investigate the effectiveness of IA.