The carcasses were spotted in aerial surveys by the territorial department of Environment and Natural Resources staff, spokeswoman Judy McLinton told the Globe and Mail.
The Mackenzie Valley area about 75 miles north of the Alberta border is accessible only by boat in the summer and hosts only a few cottages and campsites. Notices were posted at all of them that the area was closed, as anthrax can also be deadly for humans. People were told to avoid and report any carcasses they find.
McLinton said the dead bison were being soaked with formaldehyde, covered in tarps and systematically burned.
Scientists say anthrax outbreaks in the territories have been happening for many years and usually follow long spells of wet weather, which was the case this year.
The spores can lie dormant in the ground for a long time and the bison eat them through grass and other plants, the report said.
There are an estimated 2,000 bison in the southwestern part of the territory, scientists said.