Restaurant chains and beef processors defended their products’ safety Thursday after a report that an ammonia treatment thought to kill harmful germs in meat isn’t as effective as the industry and regulators believed.

The New York Times reported Thursday, citing government and industry records, that E. coli and salmonella were found dozens of times in testing for the federal school lunch program on ammonia-treated beef from Beef Products Inc. The meat was not served.

A spokesman for Beef Products, based in Dakota Dunes, S.D., said samples mentioned in the report showed traces of E. coli in 0.6 percent of the company’s production, while USDA tests found E. coli in 1.03 percent of other beef samples.

“We intend to continue as a leader in food safety efforts,” spokesman Richard Jochum said in an e-mail. He said the company’s proprietary process that treats beef trimmings with ammonia to kill bacteria is just one part of its safety and testing regimen.

No illnesses have been linked to Beef Products’ meat.

Fast-food chains McDonald’s Corp. and Burger King Holdings Inc. and agricultural conglomerate Cargill Inc. all use the meat in their hamburgers. All said they’ll keep using the meat and that their products are safe.

McDonald’s, the world’s largest fast-food chain, tests its products throughout the supply chain, said Susan Forsell, vice president of quality systems at the Oakbrook, Ill.-based company. McDonald’s said it doesn’t plan to change its relationship with the company.

“McDonald’s food safety and quality assurance standards are among the highest in the industry,” Forsell said.

Cargill spokesman Mark Klein said the company plans to continue to work with Beef Products, whose meat it uses in hamburger patties. He said Cargill does testing beyond standards set by the U.S. Department of Agriculture.