The Director of National Parks, assisted by Parks Australia within the Australian Government Department of Sustainability, Environment, Water, Population and Communities is responsible under the Environmental Protection and Biodiversity Act 1999 for managing the park in accordance with the Management Plan.
Parks Australia has an office on West Island of the Southern Atoll with a second office being operated on a part-time basis on Home Island. Currently Parks Australia has a staff of four. As well as managing Pulu Keeling National Park, Parks Australia is responsible for the application of Part 9 of the Environment Protection and Biodiversity Conservation Regulations 2000, on protected species within the Cocos (Keeling) Island Territory.
Parks Australia also manage a special protected area on Direction Island called the "Rip". This is a small section of reef with a strong tidal current from the narrow connection between the lagoon and the ocean, which is abundant with fish and coral and has a high conservation value. It was declared to protect all wildlife from any adverse impacts related to human activities.
The Cocos community are involved closely in the management of the park through their representation on the Pulu Keeling National Park Community Management Committee. This Committee consists of ten members, six of whom represent the Cocos Malay community, the Director of National Parks (or his representative), and three people from West Island.