One of Mr. Roth’s early trials involved running electricity through the trimmings to kill bacteria, Dr. Theno and others said. Mr. Roth eventually settled on ammonia, which had been shown to suppress spoilage. Meat is sent through pipes where it is exposed to ammonia gas, and then flash frozen and compressed  all steps that help kill pathogens, company research found.

The treated beef landed in Washington in 2001, when federal officials were searching for ways to eliminate E. coli. Beef Products already had one study showing its treatment would do that; another company-sponsored study by an Iowa State University professor that was published in a professional journal seconded that finding.

Mr. Roth asserted that his product would kill pathogens in untreated meat when it was used as an ingredient in ground beef  raising the prospect of a risk-free burger. “Given the technology, we firmly believe that the two pathogens of major concern in raw ground beef  E. coli O157:H7 and salmonella  are on the verge of elimination,” Mr. Roth wrote to the department.

The Food and Drug Administration signed off on the use of ammonia, concluding it was safe when used as a processing agent in foods. This year, a top official with the U.S.D.A.’s Food Safety and Inspection Service said, “It eliminates E. coli to the same degree as if you cooked the product.”

Carl S. Custer, a former U.S.D.A. microbiologist, said he and other scientists were concerned that the department had approved the treated beef for sale without obtaining independent validation of the potential safety risk. Another department microbiologist, Gerald Zirnstein, called the processed beef "pink slime" in a 2002 e-mail message to colleagues and said, “I do not consider the stuff to be ground beef, and I consider allowing it in ground beef to be a form of fraudulent labeling.”

One of the toughest hurdles for Beef Products was the Agricultural Marketing Service, the U.S.D.A. division that buys food for school lunches. Officials cited complaints about the odor, and wrote in a 2002 memorandum that they had “to determine if the addition of ammonia to the product is in the best interest to A.M.S. from a quality standpoint.”

“It is our contention,” the memo added, “that product should be labeled accordingly.”

Represented by Dennis R. Johnson, a top lawyer and lobbyist for the meat industry, Beef Products prevailed on the question of whether ammonia should be listed as an ingredient, arguing that the government had just decided against requiring another company to list a chemical used in treating poultry.