Aboriginal and Torres Strait Islander peoples suffer higher rates of food insecurity and diet-related disease than other Australians. However, assessment of food insecurity in specific population groups is sub-optimal, as in many developed countries. This study tailors the Healthy Diets ASAP (Australian Standardised Affordability and Pricing) methods protocol to be more relevant to Indigenous groups in assessing one important component of food security. The resultant Aboriginal and Torres Strait Islander Healthy Diets ASAP methods were used to assess the price, price differential, and affordability of healthy (recommended) and current (unhealthy) diets in five remote Aboriginal communities. The results show that the tailored approach is more sensitive than the original protocol in revealing the high degree of food insecurity in these communities, where the current diet costs nearly 50% of disposable household income compared to the international benchmark of 30%. Sixty-two percent of the current food budget appears to be spent on discretionary foods and drinks. Aided by community store pricing policies, healthy (recommended) diets are around 20% more affordable than current diets in these communities, but at 38.7% of disposable household income still unaffordable for most households. Further studies in urban communities, and on other socioeconomic, political and commercial determinants of food security in Aboriginal and Torres Strait Islander communities appear warranted. The development of the tailored method provides an example of how national tools can be adapted to better inform policy actions to improve food security and help reduce rates of diet-related chronic disease more equitably in developed countries.