The study of human variation has long been of interest to understand changes in the human genome that have implications in health and disease. Structural variation, large-scale genomic rearrangements, contribute the greatest diversity at a nucleotide level between any two human genomes than any other form of genetic variation. Compared to short variants, however, much of this variation is poorly characterised, particularly in ancestrally diverse populations such as Indigenous Australians. Under Indigenous governance, we characterised germline structural variation in 160 Indigenous Australian individuals from four communities and report these findings with 270 individuals from 128 populations in the Simons Genome Diversity Project, and 24 individuals from the 1000 Genomes Project. Using whole genome sequencing data, we detect 102,925 structural variants across all populations. Much of the Indigenous-specific variation detected is community-specific, but if shared is often only detected in individuals from Australia and Oceania, highlighting the importance of surveying a range of diverse communities to comprehensively characterise such variation. We also report 7,500 novel structural variants that have previously remained undiscovered in human populations. Indigenous Australians account for a large proportion (45%) of the novel population-specific structural variants, highlighting that Indigenous Australians harbour a rich set of novel variation not observed globally. Finally, we provide a description of the variation in these communities relevant for clinical applications and biomedical research and discuss the wider implications of not accounting for such variation in genomic studies. These findings highlight the importance of including diverse datasets and provide the first map of germline structural variation in Indigenous Australians at a population scale, completing part of a picture in understanding genomic variation within individuals on the Australian continent.