A significant proportion of the world's remaining dugongs (Dugong dugon) occur off northern Australia where they face various anthropogenic impacts. Here, we investigate the viability of two dugong meta-populations under varying regimes of indigenous hunting. We construct population viability analyses (PVAs) using the computer package VORTEX and published estimates of population sizes and hunting rates. In Torres Strait between Cape York and New Guinea, our models predict severe and imminent reductions in dugong numbers. Our ‘optimistic’ and ‘pessimistic’ models suggest median times for quasi-extinction of 123 and 42 years, respectively. Extinction probabilities are also high for eastern Cape York Peninsula. We demonstrate the inadequacy of reserves when harvest rates in neighbouring areas are high, identify the maximum harvest rates for meta-population stability and emphasise the urgent need for indigenous community involvement in management to establish sustainable rates of dugong harvest in these regions.