The Canadian government said it was concerned the U.S. rules were discriminating against Canadian agricultural exporters, who have lobbied hard for a legal challenge at the WTO.
"We believe that the country-of-origin legislation is creating undue trade restrictions to the detriment of Canadian exporters," Canadian Trade Minister Stockwell Day said in a statement.
The WTO confirmed receipt of Canada's complaint.
Canadian farm groups say a growing number of meat plants in the U.S. are refusing to accept Canadian cattle and hogs for processing since the Country Of Origin Labeling (COOL) law went into effect on Oct. 1.
Under country of origin labeling, Canadian cattle and pigs must be segregated in U.S. feedlots and packing plants, prompting some firms to only deal with American livestock. Canadian animals are also required to have more documentation about where they come from and, in the case of cattle, must have tags that indicate they are free of mad cow disease.
The Office of the U.S. Trade Representative in Washington could not immediately comment.
Ottawa's filing at the Geneva-based trade referee initiates a two-month consultation period between the North American neighbors. If they fail to reach a settlement, Canada can ask the WTO for a formal investigation. Such trade disputes can result in punitive sanctions, but usually after years of litigation.
Canada and the U.S. are the world's biggest commercial partners, but have battled for years over trade issues involving beef, corn, dairy and wheat. In 2006 the two countries signed an accord on softwood lumber, a key component in home-building, ending a decades-long dispute that once fueled talk of an outright trade war.
"We are committed to a respectful working relationship with our American neighbors," Agriculture Minister Gerry Ritz said, "but have always made it clear that these new regulations must not discriminate against Canadian producers."