Government funding to protect native plant communities is usually limited. For cost effectiveness, priority sites for conservation must therefore be identified and funds allocated to protect these sites according to the quantity of communities conserved per dollar of cost. In 1999, invasion of coastal vegetation in New South Wales (NSW) by bitou bush was listed as a key threatening process under the NSW Threatened Species Conservation Act 1995. In accordance with the Act, a Threat Abatement Plan (TAP) was prepared to reduce the impacts of the weed to threatened biodiversity at priority sites. In the present study, data collected for the TAP were analysed by linear programming to determine the feasibility of achieving cost effectiveness in identifying sites and allocating funds, and to explore the impact of associated economic issues on the quantity of native plant communities that are protected. In addition to the total funds and costs per site, the quantity was influenced by alternative funding policies and different site selection strategies. Allocations that recognise these issues can enhance protection outcomes, and promote the cost effectiveness of weed management.