The Commission is comprised of four directorates and an Executive Office which work collaboratively to improve the integrity of the Western Australian public sector and to help public authorities minimise and manage serious misconduct.

The Assessment and Strategy Development (ASD) Directorate is a multi-functional team working collaboratively across the Commission and the public sector through its assessment, oversight and strategic intelligence functions. ASD assesses and manages the receipt of serious misconduct allegations, which includes misconduct and reviewable police action in the Western Australian Police Force, conducts reviews of investigations conducted by public sector agencies and conducts research and analysis to inform Commission priorities and external reports. The strategic intelligence team within ASD conducts research and analysis and provides a range of intelligence products for Commission decision-makers. The focus is on broader public sector trends and issues, and identifying serious misconduct and corruption risks.

The Operations Directorate manages the Commission's investigative activities. The directorate's three units, Investigations, Electronic Collection and Surveillance, work together to proactively identify and investigate allegations of serious misconduct and reports of unexplained wealth. The focus of the Commission's investigative activity is on systemic and complex matters, many of which require the use of specialist capabilities.

The Legal Services Directorate supports the Commission in the performance of its functions under the Corruption, Crime and Misconduct Act 2003, the Criminal Investigation (Covert Powers) Act 2012 and the Criminal Property Confiscation Act 2000 by providing advice, representation, training and leadership in relation to all aspects of the Commission's operations.

The Corporate Services Directorate ensures the delivery of high quality corporate support services to the Commission. This includes the contemporary delivery of human resources, financial services, information technology and governance services, occupational safety and health compliance, and security and facilities services.

The Executive Office supports the Commissioner, Chief Executive and Commission committees, and provides administration of Commission examinations, preparation and publication of reports, facilitates risk management and audit processes, and develops internal and external communication strategies.