The New Mexico company seeking to become the first slaughter house for horses in the United States since 2007 drew complaints over a two-year period from federal food safety inspectors and state regulatory authorities over its disposal of animal remains when it processed cattle for beef.
The complaints raise questions about whether the Agriculture Department, which oversees meat processing, will approve the company's application. Under the Federal Meat Inspection Act, the grounds around a meat processing plant "must be maintained to prevent conditions that could lead to insanitary conditions, adulteration of product, or interfere with inspection."
Catherine Cochran, a spokeswoman for the U.S.D.A., said the department cannot comment on pending applications.
(Read more: USDA May Approve Horse Slaughter Plant)
The complaints included a 2010 letter to state health officials from an Agriculture Department inspector reporting that piles of animal remains were as high as 15 feet high along the back property line of the plant. "I am told that during fly season the pile literally moves due to maggots," wrote Ron C. Nelson, the district manager for the department's Food Safety Inspection Service in Denver, who took pictures of what he saw.
A. Blair Dunn, a lawyer for the company, Valley Meat, said many of the complaints, documented in e-mails and letters obtained by Front Range Equine Rescue, an advocacy group that opposes horse slaughter, were false.
"These groups have been saying all of these horrible things about my clients, and none of it was ever true," Mr. Dunn said. "If you're trying to make a point and keep something from opening, you have to be a little sensational."
(Read more: The Economics of the Taboo Against Eating Horse Meat)
He said the owners of the company in Roswell, N.M., Sarah and Ricardo de los Santos, had been struggling financially because of the sharp drop in beef cattle prices over the last three years and could not afford to have the compost and other waste hauled from the facility. In an e-mail, Mr. Dunn said there were never any environmental concerns or health hazards at the site.
However, Auralie Ashley-Marx, chief of the solid waste bureau of the New Mexico Environment Department, called Mr. Dunn's assessment "factually inaccurate," saying that after three inspections of the site in 2010, the department had issued a "notice of violation" listing Valley Meat's failure to register as a composting facility and to properly dispose of waste, as well as the improper composting of offal.
Valley Meat's application to begin slaughtering horses for human consumption, has created a furor. Horse slaughtering was effectively banned in the United States until 2011, when language prohibiting the financing of inspections of horse meat facilities fell out of an appropriations bill.
Since then, the U.S.D.A. has received applications from six companies seeking permission to start slaughtering horses, according to documents obtained through the Freedom of Information Act by Bruce A. Wagman, a lawyer for Front Range. In addition to Valley Meat, facilities in Iowa, Oklahoma, Tennessee and Rockville and Gallatin, Mo., have sought U.S.D.A. approval, Mr. Wagman said.
On Wednesday, Senator Mary Landrieu, Democrat of Louisiana; Senator Lindsey Graham, Republican of South Carolina; Representative Patrick Meehan, Republican of Pennsylvania; and Representative Jan Schakowsky Democrat of Illinois, introduced a bill to prohibit horse slaughter for human consumption and forbid the transport of horses across the border for slaughter in other countries.
The recent uproar over horse meat began in Europe earlier this year when trace amounts were found in products labeled 100 percent beef. Major food companies and restaurant chains, like Nestle and Taco Bell, pulled products off shelves and tables in 14 countries.
In describing the series of events involving Valley Meat, Ms. Ashley-Marx said her department's inspections were prompted by the letter Dr. Nelson of the inspection service sent to the New Mexico health department on Jan. 22, 2010, after a visit he had made to the plant earlier that month.
"Approximately 200 yards behind the facility, Mr. de los Santos drags dead cattle (mostly old dairy cows) and piles them on a concrete pad where he leaves them to rot," Dr. Nelson wrote. "He calls it composting, but by all appearances rotting would be more accurate."
Dr. Nelson, who is a veterinarian, said his concern was that materials that could cause bovine spongiform encephalitis, known commonly as mad cow disease, could find their way into the soil and feed.
Mr. Dunn disputed Dr. Nelson's findings, saying, "Let's get the facts straight — there never was this mountain of dead, rotting animals." He added that his clients had been working with state officials to remove the remains.
Ms. Ashley-Marx said she had not seen any carcasses, either, when she and a colleague visited the site about four months after Dr. Nelson wrote his letter. But she said the agency had identified other problems. The company did not have state permission to compost its waste materials and did not know how to properly compost animal tissue, a method called mortality composting.
Wrangling between the company and state and federal officials over permits and proper waste disposal of animal carcasses continued until last August, when New Mexico officials fined Valley Meat $86,400, the maximum penalty it can impose. The fine was later reduced to $5,000, after the company attracted new investors who helped it pay to clear the animal compost piles off its site.
Mr. Dunn blamed New Mexico Gov. Susana Martinez's opposition to horse slaughter for some of his client's problems. "Everything was moving along just fine until she got involved, and now it's all become political," he said.
Jim Winchester, a spokesman for the Environment Department, denied political influence had any bearing on the state's actions against Valley Meat.
— Written by the New York Times' Stephanie Strom