Persistent underperformance of public policy and program implementation in Aboriginal affairs is widely recognised. We analysed the results of two case studies of attempted reforms in public administration of Aboriginal primary health care in the Northern Territory, using a framework based on the institutionalist and systemic racism literatures, with the aim of better understanding the sources of implementation failure. Implementation of the agreed reforms was unsuccessful. Contributing factors were as follows: strong recognition of the need for change was not sustained; the seeds of change, present in the form of alternative practices, were not built on; there was a notable absence of sustained political/bureaucratic authorisation; and, interacting with all of these, systemic racism had important consequences and implications. Our framework was useful for making sense of the results. It is clear that reforms in Aboriginal affairs will require government authorities to engage with organisations and communities. We conclude that there are four requirements for improved implementation success: clear recognition of the need for change in ‘business as usual’; sustainable commitment and authorisation; the building of alternative structures and methods to enable effective power sharing (consistent with the requirements of parliamentary democracy); and addressing the impact of systemic racism on decision-making, relationships, and risk management.