The primary element of the institutional structure is the AANZFTA Joint Committee (FJC), which reports regularly to the consultations of the ASEAN Economic Ministers, the Trade Minister of Australia and the Trade Minister of New Zealand (known as AEM-CER Consultations) through the meetings of their Senior Economic Officials (known as SEOM-CER Consultations).  

A number of subsidiary bodies to the FJC were established under AANZFTA.  Article 1(3) of Chapter 16 of the AANZFTA Agreement also provides for the FJC to establish additional subsidiary bodies (including ad hoc bodies) and assign them with tasks on specific matters, or delegate its responsibilities to any subsidiary body.