Rabies continues to spread through eastern Indonesia and is now <500 km from northern Australia. In between the disease front and Australia lies a large susceptible population of dogs, livestock and people. Rabies was thought to have been introduced into Bali in 2007 via the illegal movement of one or more infected dogs on fishing boats, and the movement of fishing and other vessels around eastern Indonesia, East Timor, Papua New Guinea and northern Australia will likely continue its spread in this region. The first step in control is to understand the methods, routes and vehicles of transboundary disease spread. This research will describe rabies spread pathways within the region and advise on how to target surveillance systems in order to implement more effective control.