The Comptroller section is composed of four sub-sections:

• Business Applications and Policy
• Business Management and Policy
• Financial Operations and Policy
• Rent Administration and Policy

The Business Applications and Policy section focuses on the business applications used for financial purposes. This section manages and participates in the strategic development, recommendation, implementation and upgrade of the Agency’s financial systems, as well as providing training to end users. The section ensures the integrity of financial systems, manages the HAMIS - Financials module and secures linkages with the DND system.

The Business Management and Policy Section manages the Agency's business planning process and the development of financial planning documents such as the Business Plan, the Operational Plans and the Budget. In addition, the section provides ongoing financial services, analysis and advice to Agency senior management, as well as conducts the challenge function. The section produces the Agency's monthly, quarterly and year-end reviews and financial statements. The section maintains a watching brief on best practices in business management, including quality assurance and risk management, as well as develops and delivers training to CFHA staff on topics such as business planning, financial and resource management.

The Financial Operations and Policy section is responsible for the Agency's accounts. The major functions of the section include; accounts payable processing and payment certification, revenue processing and collection, preparation of the accounting trial balance, and the provision of advice on government/departmental-wide policies, practices and procedures. This includes reviewing the real and potential impact of changes on agency accounting policies and processes.

The Rent Administration and Policy section is responsible for all aspects of rent administration, including the application of rent policies, the annual rent setting process, and interaction with Canada Mortgage and Housing Corporation as the appraiser for CFHA. In addition, the section advises senior management on rent policies and their impacts on the occupants. The section ensures that the rents paid by occupants is fair and based on a market assessment.