The finding resulted in one of several official warnings between 2013 and 2016 that identified the McGartlands as “violators” — warnings that appeared on a public USDA database and that now underpin a legal battle between the Texas couple and the department. The McGartlands sued, arguing that the enforcement program denies due process to those accused of violations and breaks privacy laws by publishing personal information.

Their litigation is now being hailed by some Tennessee walking horse activists as the impetus for an abrupt USDA decision last week to pull from its public website all enforcement records related to horse soring and to animal welfare at dog breeding operations and other facilities. “This move is a direct result of the lawsuit,” reads a post on the Facebook page of TWH Facts, which is run by a prominent advocate.

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The records removal has prompted broad outcry from animal protection groups, some of which characterized it as an assault on transparency by the Trump administration. Industries regulated by the USDA, including groups representing zoos and research labs, have also been critical. So, too, have some prominent conservatives, such as Laura Ingraham.

The agency has offered little explanation for its action, saying in statements that it is the result of a review, guided by court opinions, privacy laws and current litigation, that began last year. And though the decision was made under the Trump administration — which named a longtime foe of the Humane Society of the United States to head the USDA transition — the McGartlands’ lawsuit and interviews with former agency officials and animal protection advocates suggest that changes had partially begun several months before.

Former Agriculture secretary Tom Vilsack said Tuesday that his senior staff informed him toward the end of his term that the agency division responsible for enforcing the Horse Protection and Animal Welfare acts was recommending pulling the records from the website and instead making them available via Freedom of Information Act requests. He said one rationale was that doing so would reduce staff time spent on the documents. Litigation was also a factor, he added, though he could not recall a specific court case.

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But Vilsack did not sign off on the recommendation — not because he disagreed with it but because he believed it had major implications that he didn’t have time to consider fully, he said. “There was not enough time for us to properly vet the recommendation, and I was concerned about transparency,” he explained.

Under the Trump administration, the USDA, which does not yet have a secretary, took less than three weeks to approve the removal of records that had been available for at least seven years. “I think it was probably easier to make this wholesale shutdown under the new administration,” said Delcianna Winders, a fellow at Harvard University’s Animal Law & Policy Program who is deeply familiar with the database.

Yet animal advocacy groups say access had already begun to be reduced last fall. The USDA last posted enforcement records in August, according to Eric Kleiman, a researcher at the Animal Welfare Institute who shared information about the lawsuit with The Washington Post. Other records were retroactively redacted, he said.

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Some involved SNBL, a Washington state-based company that imports primates for research. In September, the USDA filed a complaint accusing the company of violations associated with the deaths — including by thirst and strangulation — of 38 monkeys imported from Asia. Kleiman obtained the unredacted complaint through a FOIA request, and it was published on the websites of the Seattle Times and the Animal Welfare Institute.

But in November, Kleiman noted, the USDA filed a motion to seal its own complaint. It sought to redact information about SNBL’s nearly $10 million profit over two years, as well as the number of monkeys it imported and used annually — the kind of information not covered under FOIA exemptions.

The USDA’s scrubbing of records from its website has not only angered animal protection groups and journalists, who have used the documents to report on violations at Harvard University’s primate research facility, Santa Cruz Biotechnology and other places. The agency’s decision has also been criticized by some of the regulated industries.

Dan Ashe, the president and chief executive of the Association of Zoos and Aquariums, said in an interview that the removal “creates an impression that licensees by the Department of Agriculture have something to hide.” The organization Speaking of Research, which defends the use of animals in research, said the change means “researchers must devote even more resources to combating the public perception that they are not transparent.”

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Joe Watson, the CEO of Petland, which sells puppies at about 80 stores nationwide, said his company requires commercial breeders to have two years of clean USDA inspection records and depended on the database. He said Petland will now have to ask breeders to supply the reports.

“It’s always nice, I believe, to have more transparency than less,” Watson said. The change “just casts a shadow on the whole process.”

Walking horse advocates see the move as a partial victory over what they depict as overreach by a federal agency that is influenced by animal rights groups. While insisting their industry wants to comply with the Horse Protection Act, some argue that a shadow is also cast by public records that name “violators” who have not had an opportunity to defend themselves. The McGartlands’ lawsuit, now in mediation, contends that public disclosure of their warnings “indict them by innuendo and are individualized and accusatory.”

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The walking horse industry is a major target of animal-protection organizations, many of which say USDA enforcement is weak. The Obama administration sought in its final days to crack down on soring by finalizing a rule that strengthened the ban. Walking horse groups vigorously fought back, and the Trump administration has since put the rule on hold.

“This isn’t an abundance of caution,” Animal Welfare Institute president Cathy Liss said, using the USDA’s own words for its decision last week on public records. “It is capitulation to industry — a long-standing pattern for this department.”

Mike McGartland did not respond to a request for comment, nor did the couple’s attorneys. Jeffrey Howard, the publisher of the Shelbyville, Tenn.-based Walking Horse Report, also declined to comment, citing his affiliation with SHOW Inc., a co-plaintiff in the lawsuit.

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But Howard told the Shelbyville Times-Gazette that the USDA’s removal of the documents was “proper.”

“The USDA has been unfairly punishing people by listing them as violators of the HPA while never allowing those parties an opportunity for notice and a hearing,” Howard told the newspaper. “The violations statistics that the animal rights movement and [the Humane Society] have used to further their cause have been false and misleading statistics and are not violations.”