Cargill Inc. has agreed to pay $2.2 million to settle federal labor department charges of hiring discrimination at three of its meat processing plants.

The U.S. Department of Labor said Wednesday that Cargill will pay back wages and interest to 2,959 applicants who were rejected for production jobs at a turkey plant in Springdale, Ark., a beef operation in Fort Morgan, Colo., and a pork facility in Beardstown, Ill.

“This settlement will benefit thousands of workers who were subjected to unfair discrimination,” U.S. Secretary of Labor Thomas Perez said in a statement. “And it demonstrates the Department of Labor’s commitment to ensuring that everybody has a good shot at competing for good jobs.”

Minnetonka-based Cargill, one of the nation’s largest meatpackers, said it didn’t discriminate and views the Labor Department’s allegations as “unfounded and without merit.”

“After carefully weighing all options, Cargill chose to avoid the cost, business interruptions and uncertainty created by lengthy litigation,” the company said in a statement.

The Labor Department’s Office of Federal Contract Compliance Programs sued Cargill in November 2011 for alleged hiring violations at the Springdale plant. It later followed with charges of similar violations at the Fort Morgan and Beardstown facilities.

The Labor Department’s contract compliance office audits companies that do business with the federal government. Cargill has had federal contracts worth more than $1.4 billion since 2005, according to the Labor Department.

The applicants rejected for jobs — and thus covered by the settlement — were women at Springdale; women, whites and Hispanics at Fort Morgan; and whites and blacks at Beards­town, the Labor Department said. In addition to the monetary settlement, Cargill has agreed to extend job offers to 354 affected workers, as positions become available.

Cargill spokesman Mike Martin said the three meat plants are very diverse, with minorities accounting for 85 percent to 90 percent of the workforce at each.

Cargill criticized the contract compliance office’s methodology, which is based on statistical analysis of job applicants.

“We are disappointed with the way [the office] uses a mathematical model to allege violations in absence of evidence,” Cargill Senior Vice President Bill Buckner said in a statement.