Several novel viruses recently described in bats of the genus Pteropus (sub-order Megachiroptera) in Australia and southeast Asia cause encephalitic disease in animals and humans. These viruses include Hendra virus and Nipah virus (genus Henipavirus, family Paramyxoviridae) and Australian bat lyssavirus (ABLV; genus Lyssavirus, family Rhabdoviridae). Broadly, strategies for disease prevention and control in the spillover host are directed at minimising direct or indirect contact with the natural host, improving farm-gate and on-farm biosecurity, and better disease recognition and diagnosis. Additional strategies for ABLV include the use of rabies vaccine for effective pre- and post-exposure prophylaxis in humans. Effective management strategies in the natural host are predicated on an understanding of the ecology of the disease in the natural host, and the identification and avoidance of factors putatively associated with emergence, such as habitat loss, land use change and demographic shifts. A possible future management strategy for ABLV in reservoir populations is immunisation using bait or plant-derived vaccination.