The Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) aims to protect the environment and conserve biodiversity. It applies to all areas over which that the Commonwealth has jurisdiction over. This includes the Australian Antarctic Territory (AAT).

The EPBC Act provides a legal framework to protect and manage the environment, including nationally and internationally important flora, fauna, and heritage places. It also regulates actions on Commonwealth land or actions taken by Commonwealth agencies. Actions that are likely to significantly impact matters protected by the EPBC Act must be referred to the Commonwealth Environment Minister. In making key decisions in relation to a referral, the Minister will take account of the precautionary principle.

The EPBC Act also establishes the Australian Whale Sanctuary. This includes waters of the 200 nautical mile exclusive economic zone adjacent to the AAT. Regulations under the EPBC Act specify approach distances and appropriate behaviour for aircraft and vessels in the vicinity of cetaceans.