The continued spread of rabies in Indonesia poses a risk to human and animal populations in the remaining free islands, as well as the neighbouring rabies-free countries of Timor Leste, Papua New Guinea and Australia. Here we describe the development of a generic risk assessment tool which can be used to rapidly determine the vulnerability of rabies-free islands, so that scarce resources can be targeted to surveillance activities and the sensitivity of surveillance systems increased. The tool was developed by integrating information on the historical spread of rabies, anthropological studies, and the opinions of local animal health experts. The resulting tool is based on eight critical parameters that can be estimated from the literature, expert opinion, observational studies and information generated from routine surveillance. In the case study presented, results generated by this tool were most sensitive to the probability that dogs are present on private and fishing boats and it was predicted that rabies-infection (one infected case) might occur in a rabies-free island (upper 95% prediction interval) with a volume of 1000 boats movements. With 25,000 boat movements, the median of the probability distribution would be equal to one infected case, with an upper 95% prediction interval of six infected cases. This tool could also be used at the national-level to guide control and eradication plans. An initial recommendation from this study is to develop a surveillance programme to determine the likelihood that boats transport dogs, for example by port surveillance or regularly conducted surveys of fisherman and passenger ferries. However, the illegal nature of dog transportation from rabies-infected to rabies-free islands is a challenge for developing such surveillance.