The DSE manages native vegetation programs in Victoria. So with some exemptions, you must obtain a permit from the DSE if you want to collect protected native plants or if you are planning to do works or other activities that might kill, injure, or disturb protected native plants. Your application to a council for a planning permit could also be referred to the DSE if it involves removing native vegetation.

Victoria's catchment management authorities (CMAs) coordinate the development and implementation of regional catchment strategies designed to encourage ecologically sustainable development across regions (Catchment and Land Protection Act 1994 (Vic)). There are nine CMAs plus the Port Phillip Catchment and Land Protection Board. A CMA's native vegetation plan sets out the directions and priorities for vegetation management within the region. The current system allows a number of exemptions from acquiring a planning permit. While these exemptions effectively give guidance to the landholder it is wise to seek interpretation from the local council.

The Victorian Catchment Management Council (VCMC) advises the Minister for Environment and Conservation on all matters relating to catchment management, including the quality of land and water resources (Catchment and Land Protection Act 1994 (Vic)). The council is a referral body for recommendations for listings under the Flora and Fauna Guarantee Act 1988.