Dr. Brian Evans, Canada's chief veterinary officer, said the disease was found in an animal approximately six-years old. Evans said it did not enter the human-food or animal-feed systems.
The announcement comes after the CFIA's spokesman, Mark Van Dusen, said Sunday that officials were testing a "suspicious sample."
A positive test could be a blow to Canadian ranchers who had been hit hard after the United States banned Canadian cattle imports in May 2003 following the country's first case of mad cow disease. The U.S. border in July.
Mad cow disease is the common name for bovine spongiform encephalopathy, or BSE, a degenerative cattle nerve illness linked to the rare and fatal human nerve disorder Creutzfeldt-Jakob Disease.
"This case, of course, is unwelcome but it's not unexpected," Evans said. "Its age and geographic location are consistent with Canada's three previous BSE cases."
Stan Eby, president of the 90,000-member Canadian Cattlemen's Association, downplayed the impact of the test coming back positive, saying, "It will have very little impact."
"The BSE biology is much better understood now than it was 2003. We've realized it's not a human health problem. It's a animal health situation."
Eby said Canada's surveillance system is working. He said they've tested more than 70,000 cattle.
"With our active surveillance program we knew we would find a few more cases, so this should not come as any shock to our open markets," Eby said.
Canadian beef recently returned to some supermarket shelves in Tokyo following the lifting of a two-year ban on imports. Japanese officials agreed to allow beef from North America back into the marketplace, provided it came from animals under 21 months.
Entry into Japan is considered key to the long-term recovery plan of Canada's battered beef industry. The scare has cost the industry $5.7 billion.
Cattle officials have pinned their hopes on a growing appetite from Pacific Rim countries to help reduce the reliance on the U.S. market, which consumes the vast majority of this country's beef exports.
More than 150 people have died of the disease, most of them in the United Kingdom, where there was an outbreak in the 1980s and 1990s.