The Canadian Food Inspection Agency has laid 60 criminal charges against Brampton-based Maple Lodge Farms, Canada’s largest independent chicken processor, alleging violations of federal animal health regulations.

The CFIA alleges that between December 2008 and February 2009, and then December 2009 and April 2010, thousands of chickens died from exposure to cold conditions during transportation from farm to slaughterhouse, often because of proximity to a truck trailer’s floor or walls.

Two of the counts have been heard in a series of six hearings at the Ontario Court of Justice, in Brampton, which began in September. The hearings continue on Monday.

In one count, dated “on or about” Dec. 30 and Dec.31, 2008, the Crown alleges that 711 chickens, of nearly 10,000 in shipment, were “found dead on arrival” at Maple Lodge’s slaughterhouse. In the other, “on or about” Feb. 23, 2009, 1,181 chickens, of nearly 11,000, were discovered dead upon unloading at the slaughterhouse.

The first count concerns a haul of broiler chickens, which are raised solely for meat production; their breasts and thighs appear on grocery store shelves. The second refers to a load of spent hens, a term for poultry no longer capable of laying eggs, whose meat is often used in ground chicken products.

Maple Lodge, which also has a processing plant in New Brunswick, sells frozen chicken, sliced meats, chicken wieners and chicken bacon, as well as a line of halal products.

Frail and fragile after de-feathering and a lifetime laying eggs, spent hens are especially susceptible to cold exposure.

Maple Lodge called the deaths unfortunate, but emphasized the company does everything it can to ensure humane transportation of its poultry.

“We have very stringent protocols in place regarding the transportation of animals,” spokesperson Carol Gardin said. “At the end of the day, it’s not only moral and ethical considerations regarding the humane handling of the birds, there’s a financial incentive to keep the birds in the best health.”

The charges raise the question of how cold is too cold when it comes to transporting poultry. According to court transcripts, on the day the spent hens travelled, it was between -9 and -16 degrees.

In the broiler chickens’ trailer, a CFIA inspector noted “the visible presence of snow and ice in the bottom crates.” The chickens arrived at the slaughterhouse at 3:20 a.m., when the temperature was -7.

Ian Duncan, chair of animal welfare in the University of Guelph’s Department of Animal and Poultry Science, suggested that the CFIA regulate the times when chickens can be transported. In other words, if it’s too cold, keep the chickens cooped.

“There might be some temperatures below which it just might not be possible to transport chickens humanely,” Duncan said.

CFIA’s charges are a departure from its usual enforcement measure for transportation violations: levying what’s called an administrative monetary penalty. Depending on the scope of the violation, an AMP can reach $15,000.

From January to June 2011, Maple Lodge accrued 26 AMPs and paid $120,600 in fines, according to CFIA data. Between April and June, the company chalked up 22 violations, the most in Canada.

Stephanie Brown, of the Canadian Coalition for Farm Animals, believes the outcome of the hearings could set a precedent for how meat processing companies transport their animals.

“The CFIA is conceding that AMPs don’t work,” she said.

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But Liz White, director of Animal Alliance, a Toronto animal welfare coalition, said the chicken processing system — with its focus on the bottom line — is inherently inhumane.

“In order for the system to work, it has to ignore the humane aspects,” she said. “At the end of the day, the brunt is borne by the very birds we bring to our tables.”

The CFIA could not comment because the case is before the courts.