The cull began last week using sharp shooters and helicopters. Biologists hope to kill about 24 animals by spring.
Earlier this month provincial biologists announced the controversial plan to eventually cull up to 184 wolves in the Southern Selkirk Mountains and South Peace region, to protect endangered caribou.
The South Selkirk caribou are the only remaining herd that still crosses the border into the U.S., making them the most endangered mammals in the lower 48 states.
Just five years ago there were almost 50 caribou in the Selkirk herd. Now two-thirds have been killed and biologists blame wolf packs.
Tom Ethier, assistant deputy minister with the Ministry of Forests, Lands and Natural Resources, says if the wolves are not culled, the herd will be wiped out within a few years.
"We are looking at the extirpation of a caribou herd here, not 10 years out, but 3 to 5 years if this trend continues," said Ethier.
Some environmentalists have protested the cull, saying the real culprit is the government's failure to protect the caribou's habitat.
But Kootenay biologist Bob Jamieson says it's not that simple.
"If there's 18 caribou left in the southern Selkirk herd, how much habitat do we need? If there was 200 caribou, habitat might be limiting."