Matty McNair regularly retraces an ancient Inuit dog-sledding route across Nunavut's frozen Arctic tundra, guiding hardy adventurers across long, lonely stretches of sea ice, mountains and canyons. The 14-day round trip between Iqaluit and the tiny community of Kimmirut is difficult but breathtaking. It's also a glimpse back into time.

Long a fixture of the Arctic and critical to Inuit hunting and survival for generations, Canadian Eskimo dogs like Ms. McNair's are now threatened with extinction.

Ms. McNair's dogs are among the few hundred that remain of one of North America's oldest indigenous canine breeds and one of the world's rarest. Once the top dog in the Canadian North, this iconic animal has been squeezed to the sidelines by settlements and snowmobiles and a changing way of life.

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For those that remain, crossbreeding with strays is among the latest threats to their survival.

Now, Ms. McNair and other sled-dog owners are calling on Iqaluit to do more to protect Canadian Eskimo canines, urging the city to create a fenced area for the animals to keep them from getting loose and to prevent them from mingling – and breeding – with stray dogs, many of which are originally from the South.

"It's not just any old dog," Ms. McNair said of the Canadian Eskimo. She should know. Ms. McNair, who has lived in Iqaluit for 22 years, is a renowned Arctic guide and has completed a dog-sledding expedition to the North Pole.

"These are the dogs that can survive up here. If you run out of food, they keep going. They're just tough as nails."

For centuries, Canadian Eskimo dogs worked alongside Inuit, pulling them and their sleds from camp to camp and to polar-bear hunts, where the sturdy canines helped sniff out game, protect against predators and warn about precarious cracks in the sea ice. Even in blinding snowstorms, the dogs always found a way home.

As Inuit lifestyles changed in the second half of the 20th century, with many moving off the land and into government-created settlements, reliance on sled dogs began to decrease. For one, store-bought food was available. The dogs, called Qimmiq in Inuktitut by Inuit, also didn't fare well in settlements, unaccustomed to living around so many people and around so many other dogs. Their behaviour became unpredictable, prompting the police to shoot dead hundreds, perhaps even thousands, of loose sled dogs. Many others died as a result of disease outbreaks.

"One of the difficulties was that Inuit traditional practice of keeping sled dogs loose in their camps did not work in the permanent settlements. There was a clash of values and practices," noted Madeleine Redfern, who was executive director of the Qikiqtani Truth Commission, which recently examined how the move to permanent settlements changed Inuit life.

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Over time, even those families who continued to hunt began using snowmobiles to travel across the tundra. By the 1970s, Canadian Eskimo dogs were nearing extinction. Numbering an estimated 20,000 two decades earlier, their population had dwindled to about 200. Their perilous state sparked action.

In 1972, biologist William Carpenter and John McGrath, then a government economic development officer in the Northwest Territories, began a breeding project with the help of the federal government and the Canadian Kennel Club. In the northern Manitoba community of Churchill, Brian Ladoon also started breeding Canadian Eskimo dogs in the 1970s, and he still does. He has about 150 at his kennel today.

"When I started, it was sort of like a mission and now it's a congregation. I'm a priest of dogs," he said.

At the age of 60, Mr. Ladoon no longer takes his dogs sledding. Although some local residents have criticized the location of his outdoor kennel and the interaction between his dogs and polar bears, Mr. Ladoon's sled dogs are integral to the breed's preservation.

"We've kept the toughest Eskimo dogs in the world," he said.

Back in Nunavut, the dogs have made a minor comeback as a result of breeding programs, races, tourism, and requirements dog sleds be used in commercial polar-bear hunts in Nunavut and Northwest Territories.

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Ms. Redfern, a previous mayor of Iqaluit, supports creating a fenced area for the sled dogs. The proposal was introduced earlier this year when she was still on city council, but must now be revisited with the new mayor and councillors. (Ms. Redfern did not seek re-election.)

"The most important thing is to recognize [the dog's] value and support their continued use," Ms. Redfern said. "Our survival was very dependent on our relationship with Inuit sled dogs."