Indigenous health inequities persist in Australia due to a system of privilege and racism that has political, economic and social determinants, rather than simply genetic or behavioural causes. Research involving Aboriginal and Torres Strait Islander (‘Indigenous’) communities is routinely funded to understand and address these health inequities, yet current ethical and institutional conventions for Indigenous health research often fall short of community expectations. Typically, mainstream research projects are undertaken using traditional “top-down” approaches to governance that hold inherent tensions with other dominant governance styles and forms. This approach perpetuates long-held power imbalances between those leading the research and those being researched. As an alternative, Indigenous governance focuses on the importance of place, people, relationships and process for addressing power imbalances and achieving equitable outcomes. However, empowering principles of Indigenous governance in mainstream environments is a major challenge for research projects and teams working within organisations that are regulated by Western standards and conventions. This paper outlines the theoretical basis for a new Culturally Adaptive Governance Framework (CAGF) for empowering principles of Indigenous governance as a prerequisite for ethical conduct and practice in Indigenous health research. We suggest new orientations for mainstream research project governance, predicated on translating theoretical and practical attributes of real-world ethics, adaptive governance and critical allyship frameworks to Indigenous health research. The CAGF is being implemented in a national Indigenous multicenter trial evaluating the use of continuous blood glucose monitors as a new technology with the potential to improve diabetes care and treatment for Indigenous Australians—the FlashGM Study. The CAGF is a governance framework that identifies the realities of power, acknowledges the complexities of culture and emerging health technologies, and foregrounds the principle of equity for mainstream Indigenous health research.