Shooting and electrocution are inhumane
Flying-foxes are intelligent mammals with complex social lives. They communicate with more than 30 different calls.With a physiology of pain very similar to that of humans, there is no doubt they suffer if wounded or starving. 
Expert assessments, including by the RSPCA and Queensland's Animal Welfare Advisory Council, have found that shooting and electrocuting flying-foxes for crop protection are inhumane:
Because of the compelling evidence for their inhumaneness, shooting and electrocution of flying-foxes for crop protection is illegal under Queensland law .
What Queensland law requires
Queensland’s Nature Conservation Act 1992 requires that methods of killing animals for crop protection be humane and not likely to cause unnecessary suffering. The Australian code of practice for the care and use of animals for scientific purposes defines ‘humane killing’ as "the process of killing an animal with minimal pain or distress". This means that "pain or distress must be avoided and that the animal experience a rapid loss of consciousness until death occurs". 
Qld law makes this Act exempt from the Animal Care and Protection Act, and the LNP has removed the legal requirement for humanness under the Nature Conservation Act . This has damaging implications for the conservation and welfare of all wildlife in Queensland. It demonstrates beyond all doubt that the Queensland Government knows that shooting flying-foxes is intrinsically inhumane. (That is, it is near impossible to kill bats humanely by shooting).
The cruelty of shooting
Shooting a flying-fox humanely in an orchard at night is very difficult. Flying-foxes are dark and thus difficult to see and are likely to be wary and not allow a close shot. They are also a moving target as the animals are likely to be shot in flight to avoid damage to fruit. While the guidelines forbid this, it is common knowledge that the government is highly unlikely to monitor the shooting.
Shooting is typically done with shotguns, which spray relatively low-velocity pellets in a cone-shaped trajectory, and can only cause death, even if the aim is true to target, by multiple random wounding. The surface area of a flying-fox, with wings that may exceed 1 metre in diameter, is very large in comparison to the target (vital organs), which means there is a high risk of injury rather than rapid death. The body of a flying-fox is quite dense, so shotgun pellets are likely to not penetrate sufficiently to kill quickly. 
Primary producers are able to obtain a firearms licence simply because of their line of business, and there is no requirement for a skills test. There is no guarantee that a fruit grower licensed to shoot flying-foxes has the skills to do so.
Autopsies conducted on 58 dead or euthansed flying-foxes collected from a NSW orchard showed that about three-quarters of the shot flying-foxes were likely to have died several hours to days after being shot.  It is impossible for shooters to locate all injured flying-foxes for euthanasia, and many will not be motivated to do so. Less than 10% of dead animals found in the NSW orchard had been euthanased by shooters, despite a legal requirement for shooters to “locate each animal shot and promptly alleviate the suffering of any injured flying-fox by gunshot to either the head or thorax of the animal.” About one-third of the shot flying-foxes collected were still alive and the majority had to be euthanased. See here for a summary of the ‘Report on deaths and injuries to Grey-headed Flying-foxes, Pteropus poliocephalus shot in an orchard near Sydney, NSW'.
The cruelty of electrocution
It can take several minutes for a flying-fox to die on a lethal electric grid, from a heart attack due to ventricular fibrillation or from asphyxia due to paralysis of the respiratory muscles. The pain of electrocution is agonising due to sensations of intense heat, burning and suffocation.  Electricity is, after all, used for torturing humans.
Electrocution has only been permitted for humane killing of animals if the animal is first stunned by a current that flows through the brain. Because a flying-fox collides with an electric grid as it is flying, it is unlikely that current passes through the body in a way to cause rapid unconsciousness.
If a flying-fox escapes from an electric grid (as has been observed to occur), it may die after several days from electrical burn injuries or starvation. Flying-foxes treated for electrocution injuries "show signs of severe pain".  See here for more information about electric grids.
The evidence here shows that electrocution inflicts intense pain and agonizing suffering.
Justice William M. Connolly (2008), Nebraska Supreme Court, in a decision that the electric chair is a ‘cruel and unusual punishment’ (Nebraska was the last state to permit electrocution in the US.) 
The cruelty to young orphans
Spectacled, Grey-headed and Black flying-foxes generally give birth during October-December each year, coinciding with summer food availability and also with the ripening and harvest of most orchard fruits.
Flying-fox young are dependent on their mothers and suckle for up to six months after birth. For the first 3 weeks they are carried continuously by their mothers, after which they are left at the roost site while their mother forages . If they are with their mother when she is shot or electrocuted, they will die from that or from starvation, dehydration or predation. If their mother is killed while they are in the bat camp they will die from starvation, dehydration or predation. Dying can take several days.
Even if there was some way of humanely killing flying-foxes in an orchard, there is no way of locating and humanely killing orphaned juveniles in the roost site.
Welfare implications for other wildlife
Because there is compelling evidence for inhumaness of shooting and electrocution, the only legitimate way to issue damage mitigation permits for killing flying-foxes is to remove the requirement for humaneness in Queensland's conservation laws, and thus sanction cruelty to all wildlife killed for crop protection.
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LINKS & DOWNLOADS
- Why NSW Should Ban Shooting Flying-foxes (PDF)
- Report on deaths and injuries to Grey-headed Flying-foxes, shot in an orchard near Sydney, NSW (PDF)
- QCC submission to Animal Welfare Advisory Committee (2006) (PDF)
- QCC response to Animal Welfare Advisory Committee questions (PDF)
- Documents for Booth v Bosworth court case and video of electrocuted flying-foxes. (PDF)
- The effect of culling Flying Foxes
 Queensland Animal Welfare Advisory Committee (2007) Advice to the Minister for Primary Industries and Fisheries.
 Martin L. (2007) Is the fruit you eat flying-fox friendly? The effects of orchard electrocution grids on Australian flying-foxes (Pteropus spp., Megachiroptera). 10th Australasian Bat Society Conference.
 American Veterinary Medical Association (2007) AVMA Guidelines on Euthanasia.
 AWAC (2008) Animal Welfare Advisory Committee’s Recommendations. Advice to the Minister for Primary Industries and Fisheries, The Honourable Tim Mulherin.
 NSW Flying-fox Licensing Review Panel (2009) Report to NSW Department of Environment and Climate Change.
 Expert Working Group of the Animal Welfare Committee of the National Health and Medical Research Council (2008) Guidelines to promote the wellbeing of animals used for scientific purposes. Australian Government.
 Booth C. (2007) A response to questions by the Animal Welfare Advisory Committee, Queensland Conservation Council, May 2007. Various references therein.(PDF download)
 Divljan A, Parry-Jones K, Eby P (2009) Report on deaths and injuries to Grey-headed Flying-foxes, Pteropus poliocephalus shot in an orchard near Sydney, NSW.
 Hillman H (1993) The possible pain experienced during execution by different methods. Perception 22: 745 - 753
 Hangar J. (2007) Director of Veterinary Services, Australian Wildlife Hospital. Affidavit evidence fin Booth v Frippery & Ors. “I believe that it is a proper assumption that flying foxes affected by electrocution injury and burns suffer pain of a similar magnitude to that suffered by humans with similar injuries.”
 Justice William M. Connolly (2008), Nebraska Supreme Court, for the majority in a 6-to-1 decision.
 See here.
 Nelson J. (1965). Behaviour of Australian Pteropodidae (Megachiroptera). Animal Behaviour. 13:544-557.
Authorised by Des Boyland, 95 William Street, Brisbane Qld