INTRODUCTION: Contouring has become an increasingly important aspect of radiation therapy due to inverse planning, and yet is extremely time-consuming. To improve contouring efficiency and reduce potential inter-observer variation, the atlas-based auto-segmentation (ABAS) function in Velocity was introduced to ICON cancer centres (ICC) throughout Australia as a solution for automatic contouring. METHODS: This paper described the implementation process of the ABAS function and the construction of user-defined atlas sets and compared the contouring efficiency before and after the introduction of ABAS. RESULTS: The results indicate that the main limitation to the ABAS performance was Velocity's sub-optimal atlas selection method. Three user-defined atlas sets were constructed. Results suggested that the introduction of the ABAS saved at least 5 minutes of manual contouring time (P < 0.05), although further verification was required due to limitations in the data collection method. The pilot rollout adopting a 'champion' approach was successful and provided an opportunity to improve the user-defined atlases prior to the national implementation. CONCLUSION: The implementation of user-defined ABAS for head and neck (H&N) and female thorax patients at ICCs was successful, which achieved at least 5 minutes of efficiency gain.