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A federal food inspector at Rancho Feeding Corp. repeatedly criticized practices inside the Petaluma slaughterhouse now at the center of an international meat recall and an ongoing criminal investigation, according to union officials.

The inspector at Rancho thought her supervising veterinarian had approved "questionable" dairy cows for slaughter during a five-month period last year, according to a union official who said he has reviewed documents detailing the inspector's accounts.

The federal inspector also alleged that employees at the Petaluma plant had mistreated animals, improperly discharged wastewater and subjected her to harassment, said Paul Carney, president of the Western Council of the National Joint Council of Inspection Locals, the federal meat inspectors union.

The inspector's concerns, which upset plant management, were often ignored by her supervisor at the U.S. Department of Agriculture, Carney said, citing documents that he has reviewed. She was moved to another plant in November, he said.

He criticized the USDA's Food Safety Inspection Service, saying the agency did not support the inspector or intervene at Rancho to resolve problems at the plant.

"I think the plant was allowed to have too close of a relationship with FSIS management, but FSIS management is to blame for that," said Carney, a former inspector.

It is unclear what role, if any, the incidents Carney described may have played in the events leading up to the recall and ongoing investigations by the U.S. Department of Agriculture, its Office of Inspector General and the U.S. Attorney's Office.

The investigations are focusing on events that allegedly occurred outside the presence of USDA inspectors assigned to the plant, Rep. Jared Huffman, D-San Rafael, said Monday after a telephone briefing from Agriculture Secretary Tom Vilsack. The USDA said it is examining "the company's intermittent circumvention of inspection requirements."

Robert Singleton, one of Rancho's co-owners, said the company did not attempt to get around inspection rules and never harvested animals without an inspector on site. He denied any mistreatment of the USDA inspector.

"No, she wasn't harassed," Singleton said.

His partner, Jesse "Babe" Amaral, has not returned telephone calls seeking comment.

The inspectors union has tussled for years with the USDA over food safety protocols. The rules, according to union leaders, give slaughterhouse officials too much control over the safety and inspection process. More recently, the inspectors union has said staffing levels are unacceptably low.

A top union official last week suggested that a shortage of inspectors may have played a role in the Rancho recall. The inspectors are stretched too thin and do not have enough time to properly examine meat, said Stan Painter, chairman of the National Joint Council of Food Inspection Locals.

Vilsack, however, told two North Bay congressmen last week that the Rancho recall did not reflect in any way a failure of the inspection system, Huffman said. The secretary rejected suggestions that suspect meat got into the food supply due to a shortage of inspectors.

The USDA has said Rancho "processed diseased and unsound animals" without a full inspection. Rancho is now recalling all 8.7 million pounds of beef and veal it processed in 2013. No reports of illness have been linked to the meat.

The USDA's description of the meat in question is telling, said Seattle attorney Bill Marler, a specialist in food safety cases.

"The words used — 'diseased' and 'unsound' — usually what that means is that there were animals that were non-ambulatory, they were downers, with visible defects, and that somehow they made it on to the kill floor without inspection," said Marler, who publishes Food Safety News, an online news site.

The federal food inspector assigned to Rancho repeatedly questioned the practices inside the plant over a five-month period prior to November, according to Carney and Painter.

"She was speaking out and exposing that there were problems," Carney said.

He declined to reveal the inspector's name or provide copies of the documents detailing her accounts. He said the documents include correspondence between the inspector and her supervising veterinarian, and a sheaf of complaints about the inspector made by Rancho management to the USDA. He summarized her allegations in a series of interviews with The Press Democrat.

The USDA has not yet responded to a Freedom of Information Act request by The Press Democrat for inspection reports and other records related to the Rancho plant.

The food inspector alleged that her supervisor, a USDA public health veterinarian assigned to Rancho, was approving dairy cow carcasses that she believed should have been rejected, Carney said.

"She thought he was passing carcasses that were questionable," he said.

"She would tag animals for the PHV (public health veterinarian) and what she thought sometimes were cancerous, the vet would pass," he said. "And she can't question the vet."

The food inspector also said that her supervising veterinarian ignored many alleged violations of federal regulations that she had identified and brought to his attention, Carney said. The veterinarian refused to write up many of the alleged violations or allow her to write the noncompliance reports, Carney said.

"He didn't want them, so he didn't authorize her to write too many," he said.

In one incident, Carney said, the food inspector reported that water was blasted into a calf's nostrils to make it more compliant. That would be considered inhumane treatment under slaughter guidelines, said Temple Grandin, a Colorado State University animal science professor who wrote the American Meat Institute's guidelines for humane slaughter and handling.

In another incident at Rancho, Carney said, a dairy cow had not been properly rendered unconscious before it was hung from a hook to bleed out. The inspector asked employees to remove the animal from the hook but they instead reportedly shot it with a bolt gun several more times to stun it, Carney said.

"Which is not a bad thing by itself, but it should be more controlled, damn it," he said.

The inspector also raised alarms about improper discharges of plant wastewater into nearby fields, Carney said.

The USDA reassigned the inspector to another plant in November, Carney said. The veterinarian assigned to Rancho retired within the last two months, the union leader said. He does not know the full name of the veterinarian, he said.

A USDA spokesman would not comment on the allegations described by Carney, saying they were personnel matters. He declined to identify the inspector or her supervising veterinarian.

"I have no idea and we would not comment on it either way," said Richard McIntire, a spokesman for the USDA's Food Safety and Inspection Service.

Carney said the food inspector would not agree to an interview because she was fearful of retaliation by her employer. He declined to name her, saying she has asked him not to.

He said he has documents buttressing her account of her actions but he could not make them available until the inspector decides how to proceed.

The Petaluma slaughterhouse ceased operations in early February as it wrestled with the recall effort, which its owners said was pursued out of an "abundance of caution." The plant is now being sold to Marin Sun Farms, a gourmet meat producer.

Since January 2012, there have been at least 12 other recalls of meat products that did not receive complete inspections, according to FSIS records and Food and Water Watch, a consumer advocacy group in Washington, D.C. The Rancho Feeding recall is by far the largest.