More than 100 unwanted dogs have been put down by the Masterton District Council in the year to June 30, including 89 that were shot by firearm.
The council said its policy was to have dogs euthanised by a vet whenever possible, but shooting was necessary in some cases.
Masterton District Council chief executive officer Wes ten Hove said shooting was not the "preferred method" for destroying dogs.
But in some instances, such as when a veterinarian was unavailable or there were concerns for staff or animal safety, they needed to be shot.
The dogs were buried in a designated special waste area at the Nursery Rd transfer station, which was available to residents wanting to dispose of an animal.
Mr ten Hove said dogs were euthanised when owners could not be identified and the animals were not deemed suitable for re-homing.
In the year ending June 30, 207 dogs were returned to their owners, 89 dogs were euthanised by firearm and 20 were euthanised by veterinarian Heidi Ward-McGrath, from Vetcare. A small number were re-homed or passed to the SPCA for re-homing.
Dr Ward-McGrath, who no longer provides veterinary services to the council, has criticised the use of firearms to put dogs down, and the manner of their disposal.
She spoke to a meeting of councillors about her concerns this month.
"Those are people's pets and people care greatly about animals and animal welfare. It's been very distressing to find out what's happened and the sheer numbers it's happening to," she said.
Mr ten Hove said the council's policy was consistent with the Animal Welfare Act and the Code of Welfare for Dogs: "I am satisfied that my guys adhere to the council policy for the humane destruction of the dogs that we have. Our first preference will remain that we use a vet."
The Carterton District Council euthanised 14 dogs in the the 2011/12 year. Animal-control officer Robert Millar said dogs were shot or taken to a veterinarian - it depended on circumstances.
That had been the council's policy for more than 40 years.
Mr Millar said shooting was often less traumatic than taking the dog to the vet, and other methods could be "messy" or "cruel".
"It's a quick and effective way of destroying a dog," he said.
The bodies were disposed of in an offal hole on council property.
South Wairarapa District Council planning and environment manager Glenn Bunny said dogs were euthanised with a firearm in all cases. The council had a long-term arrangement with a landowner to dispose of the dogs.
Mr Bunny said 40 to 50 dogs arrived at the pound a year, and eight had been put down in the past year.
Wairarapa SPCA manager Val Ball said shooting was not the SPCA's choice, but was humane: "If it's done right, it's not a problem."
Aspects of Dr Ward-McGrath's work for the council are disputed by the parties, and the council said she had not been used for veterinary services since July 31.
Mr ten Hove said the Nursery Rd facility had been used by Vetcare for disposing of dogs in the past.