This paper reviews the advocacy role of Aboriginal community controlled health services (ACCHSs) in the development of Aboriginal health policy over the past 30 years, with a specific focus on the recent changes in Commonwealth funding and administrative responsibility - the transfer of Aboriginal health service funding from the Aboriginal and Torres Strait Islander Commission (ATSIC) to the Office of Aboriginal and Torres Strait Islander Health Services (OATSIHS) within the Commonwealth Department of Health and Ageing (DoHA), and the development of policies aimed at Aboriginal health services accessing mainstream (Medical Benefits Scheme [MBS]) funds. The outcomes of this policy change include a significant increase in funding to Aboriginal primary health care (PHC), the inclusion of ACCHSs in collaborative strategic relationships, and the development of new arrangements involving regional planning and access to per capita funds based on MBS equivalents. However, the community sector remains significantly disadvantaged in participating in this collaborative effort, and imposed bureaucratic processes have resulted in serious delays in releasing funds for actual services in communities. Government agencies need to take greater heed of community advocacy, and provide appropriate resourcing to enable community organisations to better direct government effort, especially at the implementation phase. These remain major concerns and should be considered by non-health sectors in the development of new funding and program development mechanisms in the wake of the abolition of ATSIC.