To examine Indigenous Governance of Data processes in Australian clinical registries. Audit (via desktop review and interviews) of registries in the Australian Register of Clinical Registries from 17 January 2022 to 30 April 2023. The number of clinical registries collecting ethnicity data, reporting Aboriginal and/or Torres Strait Islander representation on registry governance or steering committees, and reporting human research ethics committee approval. A total of 107 clinical registries were reviewed. Of these registries, 65 (61%) collected ethnicity data; when these were grouped by geographical coverage, those most likely to collect ethnicity data were binational (24/40 [60%]), national (19/26 [73%]) or state based (19/26 [73%]). Of the registries that collected ethnicity data, 29 (45%) classified their ethnicity item as Aboriginal and/or Torres Strait Islander. Only eight clinical registries (7%) reported Aboriginal and/or Torres Strait Islander representation on their governance or steering committees. Human research ethics approval was reported in 94 registries (88%), with only 11 (12%) having Aboriginal human research ethics committee approval. Significant variability is evident in clinical registry recording of Indigenous governance of data, meaning that Aboriginal and Torres Strait Islander communities remain invisible in data which is used to inform policy, clinical models of care, health services and initiatives. Radical change is required to facilitate meaningful change in quality indicators for clinical registries nationally.