Even in statistically advanced countries, estimates of subnational international migration are often lacking. In Australia, immigration and emigration estimates are regularly published for the States and Territories, but not for finer geographical scales. Some sub-state immigration data are available from the census, but equivalent emigration data do not exist. This paper proposes a method for creating sub-state immigration and emigration estimates for Australia which are consistent with state-level international migration statistics published by the Australian Bureau of Statistics (ABS). International migration flows for the period 2006–2011 were estimated for 49 sub-state regions comprising State/Territory capital city regions and large regions outside the capitals. Use was made of ABS state-level international migration statistics disaggregated by visa/citizenship category, and detailed census data. Immigration was simply distributed to regions on the basis of census immigration flows. The estimation of emigration was more complex: state-level flows by visa/citizenship category were distributed spatially according to different combinations of census variables. The methods are shown to produce plausible estimates of immigration and emigration, and thus net international migration, at the sub-state scale. These estimates should prove useful for improving our knowledge and understanding international migration flows in Australia at the regional scale, and for setting population projection assumptions.