Unlike many other Australian parks and reserves there is no permanent or frequent on-site management presence in the Heard Island and McDonald Islands Marine Reserve.

The Reserve is administered and managed by the Australian Antarctic Division (AAD), on behalf of the Director of National Parks.

The Director of National Parks is responsible for managing all of Australia’s Commonwealth-managed parks and reserves. The delegation of responsibilities for HIMI reflects the AAD's continuing role and responsibilities for management and administration of the HIMI Territory (including the HIMI World Heritage area) on behalf of the Australian Government and the AAD’s long and significant historic involvement in the HIMI region and in the protection and conservation of its environment.

The Director of National Parks publishes a Report each year for the suite of Australian Commonwealth-managed parks and reserves.

To help manage such an isolated place, the AAD maintains close relationships with all visitors, and with other agencies with operational presence in, or responsibilities for, the HIMI region. Such agencies include: