A population survey of the caribou on Nunavut’s Southhampton Island is scheduled to begin Thursday.

It's the third year in a row that hunters and government biologists are counting the animals.

There's concern because the herd has shrunk dramatically in recent years. Numbers dropped to about 7,500 animals in 2011 from about 30,000 in the late 1990s.

Last year's survey found a further drop, to somewhere between 5,000 and 6,000 animals.  

Hunters on the island agreed last year to limit the harvest to 1,000 animals.

Noah Kadluk, chair of the Coral Harbour Hunters and Trappers Organization, said the decision to restrict the harvest was difficult for many hunters.

"Of course they didn't like it, but we don't all agree with what has to be said, especially with wildlife," he said.

"But people have to understand that we're on an island and we have to manage our caribou herd if we're going to keep them on the island."

Caribou have been wiped out on Southhampton Island before. The herd was hunted to extinction in the 1950s.

Animals were later brought over from nearby Coats Island to reestablish a herd.

It's not clear what's driven the current decline but biologists say the population was hit hard by the disease brucellosis, making it more vulnerable to hunting pressure.

Kadluk said it appears the population may have stabilized in the last year, but it's hoped the new survey will provide a clearer picture.

Each aerial survey costs more than $100,000, but despite the cost, government biologists say the data is necessary to manage the herd.

"It is a difficult thing when harvest is being restricted for people that rely on caribou meat as part of their household food that they're used to. And it's healthy country food," said Mitch Campbell, the Nunavut government's caribou biologist in the Kivalliq region. 

"To have to sort of take less of that, people want to be absolutely certain about the numbers that are being used to guide the setting of those kind of restrictions."

The aerial survey should be finished within the next week or two. The goal is to have results in time to set this year's harvest quota by July 1.