Border Protection Command is commanded by a Rear Admiral seconded from Defence who, as Commander Border Protection Command (CBPC), has operational control of both Australian Defence Force (ADF) and Customs and Border Protection assets assigned to civil maritime security operations. CBPC exercises this command through deputies located in two headquarters; Border Protection Command Headquarters in Canberra, which coordinates Customs and Border Protection assets via the Australian Maritime Security Operations Centre, and through HQJTF639 in Darwin, which coordinates the ADF assigned assets. This structure is illustrated below.
- Australian Customs and Border Protection Service;
- the Department of Defence;
- Australian Fisheries Management Authority; and
- Department of Agriculture.
Commander, Border Protection Command is a Royal Australian Navy officer of two star rank. The current Commander is Rear Admiral Michael Noonan, AM, RAN. The Commander is supported by:
- Deputy Commander, Border Protection Command;
- Deputy Commander, Northern Command Headquarters (JTF639);
- Chief of Staff;
- Command Legal Officer;
- Director Governance and Command Support;
- Director Operations;
- Director Intelligence;
- Director Strategy, Engagement & Counter Terrorism;
- Director Operational Planning; and
- Regional bases in Cairns, Darwin, Broome and Thursday Island.