The U.S. Department of Agriculture has found "systemic" inspection and sanitation problems during its most recent audit of Canada's meat, poultry and egg inspection systems, issues American officials say "raise significant questions about the Canadian system."

The most "significant" concern, U.S. auditors said, was that Canadian government plant inspectors were not checking for residual feces and digestive waste materials on each carcass in slaughterhouses prior to export.

"Auditors noted that government inspectors appear to not be conducting carcass-by-carcass post-mortem inspection to ensure freedom from contamination," noted the audit. Conducted in 2016, it was released this spring but garnered little attention.

"This could be a significant finding for the [U.S. Food Safety and Inspection Service] and could be inconsistent with [U.S.] requirements."

"Post-mortem inspection procedures that do not ensure carcass-by-carcass inspection . . . raise significant questions about the Canadian system," American officials wrote in the audit.

The audits were conducted in September 2016 in slaughterhouses in Alberta, British Columbia, Ontario and Quebec and shared with the Canadian Food Inspection Agency in April.

U.S. requirements on imported meat

The United States requires carcasses to be inspected by a government inspector to confirm they aren't contaminated before they are stamped "inspected and passed." The rule applies both to meat from the U.S. and carcasses imported into the country.

The U.S. government could temporarily ban Canadian plants from exporting their products to the United States if the requirements aren't met.

The CFIA declined CBC News' request for interview, but issued a statement insisting Canada's food system is safe.

"Both Canada and the U.S. have rules that prohibit the production of meat from carcasses that are contaminated," said CFIA spokeswoman Maria Kubacki. "Both countries have high standards for food safety. Canada and the U.S. have different approaches to verify that carcasses are free of contamination, and neither Canada nor the U.S. tolerates contamination on food animal carcasses."

But the American audit pointed out about 60,000 kilograms of Canadian meat and poultry products were rejected by the United States for "various public health reasons" between 2013 and 2015.

Meat contaminated by manure, ingesta (food from the animal's digestive system) or other bodily fluids such as milk is the primary way for pathogens, such as E. coli, to spread.

An E. coli outbreak at an XL Foods plant in southern Alberta in 2012 was detected by U.S. inspectors and led to the largest meat recall in Canadian history. Eighteen people in Canada got sick from eating the beef. (XL Foods was sold in 2013 to JBS South America of Brazil.)

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Cattle graze beside the former XL Foods' Lakeside Packers plant located in Brooks, Alta. E. coli detected in meat from XL's plant led to the largest meat recall in Canadian history in 2012. (Larry MacDougal/Canadian Press)

The CFIA statement added that discussions with its U.S. counterparts to address the U.S. concerns are "ongoing."

"Our goal is to achieve a common understanding about how two inspection systems meet the same food safety outcome," Kubacki said.

Bob Kingston, president of the Agriculture Union representing food inspectors in Canada, said he is "not surprised at all" by the American audit results, pointing to a need to hire more front-line inspectors.

Union says resources stretched

"Canadians should be disappointed and angry," Kingston said in an interview with CBC News.

"If you take a look at almost every single deficiency in this agency for the last decade, they all go back to resources," he said. "At the end of the day, CFIA has an extremely competent group of people who are stretched beyond their limit."

"The inspection staffs go home with their fingers crossed hoping they're not going to get some bad news because of something they missed," Kingston said.

In its spring budget, the Liberal government promised an additional $149 million over five years, starting with $37 million this year, "to renew core food safety inspection programming delivered by the Canadian Food Inspection Agency and Health Canada."

The 2016 U.S. audit came two years after another audit raised concerns about meat processing in Canada, particularly over testing for Listeria monocytogenes, the same bacteria responsible for a listeriosis outbreak in deli meats linked to 22 deaths in 2008. American officials say CFIA has since resolved those issues.