Cleanup costs at a single northern mine next to Great Slave Lake are ballooning so high they are forcing Ottawa to rethink plans for thousands of contaminated sites across the country.

Documents obtained by northern environmentalists show the government expects the cost of cleaning up the Giant Mine just outside Yellowknife to be nearly a billion dollars — perhaps the largest single environmental cleanup in Canada and paid for entirely by taxpayers.

Initial estimates for safely dealing with the huge site, which includes a toxic smorgasbord of buildings, tailings ponds and a quarter-million tonnes of arsenic stored underground, were about $488 million.

A federal progress report on the project says costs have increased as more has become known about the scale of the problem.

“The increase in estimated costs occurred as a result of the normal progression through the preliminary phases of the remediation project (... increased site information and detail obtained over time),” the report says.

Rising labour and equipment costs are also part of the problem. So is the current state of the mine, which is so bad that emergency measures need to be taken this summer before large amounts of arsenic start escaping from collapsing buildings.

The official price tag of $903 million could get higher yet.

“There is a potential for the total project cost estimates to increase over time,” says the report, which uses figures as of March 2012.

The costs are already squeezing funding for other federal cleanups.

The Giant Mine remediation project is funded out of a federal program for contaminated sites. Beginning in 2005, a total of $3.6 billion over 15 years has been earmarked for the program.

That was supposed to be enough for 6,765 known toxic sites, including 2,709 “priority” sites. They include the Lennard Island lighthouse off the coast of Vancouver Island, the Happy Valley-Goose Bay air force base in Labrador and Rock Bay in Victoria Harbour. Cleaning up the Faro Mine in the Yukon alone is expected to cost up to $590 million.

Contaminants found on the sites vary widely, but most common are fuel residues, metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs).

Environment Canada spokesman Mark Johnson said there’s enough money in the kitty for immediate work.

“There is currently sufficient funding available to cover the cost of planned remediation activities at high priority sites,” he said in an email.

Other sites, however, may have to wait.

“The government of Canada will re-examine its approach to identifying the highest priority sites for funding.”

The Giant Mine is getting so bad that the federal government has asked the N.W.T.’s environmental regulator for emergency approvals to clean up the crumbling site.

About 3,600 cubic metres of arsenic and arsenic-contaminated material remain in surface structures — uncontained and in many cases exposed to the elements.

Photographs from the site show piles of arsenic dust lying exposed inside the old flues that used to carry it underground. Those flues are pulling away from the building they were attached to and slowly collapsing as concrete and wood pillars that held them up rot away.

Snow blows freely through derelict walls and roofs onto arsenic-contaminated equipment. Asbestos insulation waves in the wind as it flakes off old pipes and buildings.

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Underground, arsenic-stuffed caverns are in danger of falling in from the surface or collapsing into mined-out areas below. The mine’s main smokestack is crumbling.

Arsenic poisoning starts with headaches, confusion, severe diarrhea and drowsiness. When the poisoning becomes acute, symptoms may include diarrhea, vomiting, blood in the urine, cramping muscles, hair loss, stomach pain and more convulsions.

Continued poisoning leads to a coma followed by death.

The cleanup will be so dangerous that buildings will have to be sealed off as they are demolished and removed. Workers would have to wear full haz-mat suits and breathe supplied air.