Flying-foxes come into conflict with fruit growers when they raid fruit crops in response to limited native food resources. A standard technique used by fruit growers to deter flying-foxes has been to shoot the animals as they enter the orchard. This activity has been regulated by National Parks and Wildlife Service (NPWS) since the protection of flying-foxes in 1986. A NPWS Policy was developed on this issue in 1998. It provides for licences to be issued to harm a limited number of protected species by gunshot only. The policy does not cover threatened species.

The recent change in the conservation status of the Grey-headed Flying-fox from protected to vulnerable means that the NPWS policy must be adapted to address damage mitigation of a threatened species. The NPWS has considered a number of alternatives in its management strategy including ending licensed harm to flying-foxes, issuing licences under the Threatened Species legislation and encouraging farmers to prepare property management plans. The preferred NPWS position is to continue to issue licences under the National Parks and Wildlife Act 1974 for a further three years during which time farmers are expected to take all reasonable means to adopt non-lethal deterrent strategies. Important aspects of this new policy are ensuring that licensed damage does not constitute a threat to the long term survival of the Grey-headed Flying-fox, and improving compliance with the policy so that all harm may be quantified and the impact on the State-wide population properly assessed and managed.