The APVMA is an Australian government statutory authority, employing approximately 150 people. The authority exists within the portfolio of the Minister for Agriculture.

The APVMA is a corporate Commonwealth entity constituted by an executive manager, the Chief Executive Officer, who has responsibility for the management and governance of the authority. As of 1 July 2014, the APVMA is subject to financial regulation under the?Public Governance, Performance and Accountability Act 2013?(ComLaw). APVMA staff are engaged under the?Public Service Act 1999?(ComLaw).

Prior to 1 July 2007 the APVMA's focus and strategic direction was determined by a Board of Directors. The reform of the APVMA's governance arrangements to an Executive Management model followed an Australian Government review of the corporate governance arrangements for statutory authorities and office holders—Review of the Corporate Governance of Statutory Authorities and Office Holders (the 'Uhrig Review'). Government policy for the corporate governance arrangements for statutory authorities is set out in the document?Governance Arrangements for Australian Government Bodies.