"Macho" dog control officers are routinely shooting dogs as a means of euthanasing them, while other councils use bolt-guns and one uses a gas chamber.
Thousands of unwanted dogs and puppies are killed using firearms or bolt-guns each year by councils - often as a way of saving money.
The "messy" methods are legal, but have been criticised as traumatic for both dogs and the officers involved, with the animals sometimes needing a second shot to be finished off.
The practice also flies in the face of the SPCA's "preferred" method, which is by intravenous injection by a registered vet.
Institute of Animal Control Officers president Les Dalton said firearms and bolt-guns were widely used, particularly away from the main urban centres.
"I'm well aware there are a lot of macho officers out there using firearms and they will continue to do so.
"I've been disturbed for some time about it . . . it's more traumatic on the officers for one, because when the animal is shot there's a lot of bleeding.
"And there's always a chance that the dog can move its head and the first shot might not work."
Bolt-guns - which shoot a retractable steel bolt - could be very messy and were not accurate, he said.
Mr Dalton, who is also head of dog control for the Hutt Valley and Wellington regions, said councils there had long used injection by vets. Porirua and Kapiti Coast councils also use vets.
"I think today there's better ways [than shooting]. It isn't illegal, but it's not a preferred method in this 21st century."
Euthanased dogs are nearly all unregistered, unchipped and deemed unsuitable for rehoming.
A survey of 46 councils obtained by The Dominion Post shows 15 exclusively use firearms to euthanase unwanted dogs, while 12 others used both firearms and vets.
Six councils use bolt-guns, while 14 use a vet. One council - Wanganui - uses a carbon monoxide "chamber".
Wanganui District Council animal control team leader Bernie Compton said the dogs were put into a dark chamber into which carbon monoxide was fed. They were left for seven minutes, in which time they went to sleep before dying.
"This method is less stressful for our animal control staff, as well as the animals themselves," he said.
South Wairarapa District Council planning and environment manager Glenn Bunny said cost was a "key component" of its choice to use a firearm.
"A bullet costs 50 cents or a couple of bucks, versus a vet, which costs between $120 and $150. So it's a pretty big difference."
A Gisborne District Council spokeswoman said it put down about 40 dogs each month with a bolt-gun. The method was considered more cost-effective than using a vet, and safer than using a rifle.
SPCA national inspectorate manager Alan Wilson said any humane method that did not cause unnecessary suffering was acceptable.
The SPCA's preferred method was injection by registered vet, but shooting was often chosen because of its lower cost, he said.
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