Large-scale projects that develop perpetual community resources, such as UK Biobank, 1000 Genome Project, and the Human PanGenome Reference, play an increasingly important role in biomedical research and precision medicine. The National Centre for Indigenous Genomics (NCIG) is establishing genomic reference resources and related biospecimens from Indigenous Australians. It is an example of a community resource built to enable broad-scale representation of ancestrally diverse populations to enable equitable benefits of genomics for all humans, irrespective of their ancestry. In the first phase, we have established deeply trusted relationships with four Indigenous communities; 684 individuals (10% of population) have donated their genomic data and samples into the growing NCIG collection. We have begun generating reference genomes leading to telomere-2-telomere assemblies. In addition, whole-genome sequence data from 160 individuals using ONT long reads and Illumina short reads has revealed distinct genetic diversity missing from global resources and specific to Indigenous communities. We have established first that the unique genetic diversity of Indigenous Australia will require modification to data analysis workflows to discover genetic variations accurately. Second, many more Indigenous communities would have to be included in genetic reference resources to comprehensively ascertain genetic diversity to benefit all Indigenous Australians. The next phase of NCIG, under Indigenous governance backed by federal statutory powers, will enable integration of these genomic resources into clinical practice in coming years.