The video appears to show workers bungling the slaughter of cows struggling to walk and even stand. Under federal regulations, sick animals cannot be slaughtered for human consumption.
The investigation will determine whether sick cows were slaughtered and whether meat products from the company should be recalled, said Justin DeJong, a spokesman for the USDA Food Safety Inspection Service.
The agency suspended operations Monday at Central Valley Meat Co. in Hanford after receiving the video Friday from the animal welfare group Compassion Over Killing. The footage shows animals bleeding and thrashing after being repeatedly shot in the head with a pneumatic gun in unsuccessful efforts to render them unconscious for slaughter.
Federal regulations say that to avoid unnecessary suffering during slaughter, animals must be rendered unconscious by a single shot to the head from a pneumatic gun that fires a bolt through the skull to pierce the brain.
In-N-Out Burger, a fast food chain, severed its ties with the company after learning about the situation. Mark Taylor, chief operating officer, said on Tuesday that the company acted immediately upon becoming aware it.
"As soon as we became aware of the allegations regarding Central Valley Meat Company and their handling of cattle, we immediately severed our supplier relationship with them. In-N-Out Burger would never condone the inhumane treatment of animals and all of our suppliers must agree to abide by our strict standards for the humane treatment of cattle," Taylor said to The Associated Press in a written statement.
In-N-Out's agreement with suppliers prohibits companies from shipping beef from sick animals. The agreement also includes standards on humane treatment of animals.
The USDA said investigators are trying to determine whether the cows in the video were just lame or sick, which would render them unfit for human consumption.
"That's the main issue right now," said DeJong of the USDA's Food Safety Inspection Service.
Central Valley Meat Co., owned by Brian and Lawrence Coelho, declined to comment on the video, saying company officials had not seen it.
"We were extremely disturbed to be informed by the USDA that ... our plant could not operate based upon a videotape that was provided to the department by a third-party group that alleged inhumane treatment of animals on our property," said a company statement.
Brian Coelho added, "Our company seeks not just to meet federal humane handling regulations, but exceed them."
The video taken by an undercover investigator for Compassion Over Killing also shows cattle lying in pens unable to move, and at least one unable to stand to leave a stock transportation trailer.
Some clips show cattle with swollen udders that are unable to keep their legs under them. Other footage shows a downed cow trembling and unable to stand even as workers try to pull her up by the tail.
Within hours of seeing the video, the USDA's Office of Inspector General sent investigators who found evidence of "egregious inhumane handling and treatment of livestock." The possibility that animals were being inhumanely treated caused officials to shut down the plant while the investigation unfolds.
The USDA had at least two inspectors stationed at the site, and federal officials, when asked whether there was evidence the inspectors had neglected their duties, said the investigation is ongoing.
The USDA received hours of videotape from the Washington D.C.-based animal welfare group, which said its undercover investigator was employed by the slaughterhouse and made the video over a two-week period in June and early July.
Four minutes of excerpts the animal welfare group provided to The Associated Press showed cows being prepared for slaughter. One worker appears to be suffocating a cow by standing on its muzzle after a gun that injects a bolt into the animal's head had failed to render it unconscious.
In another clip, a cow is still conscious and flailing as a conveyor lifts it by one leg for transport to an area where the animals' throats are slit for blood draining.
"The horror caught on camera is sickening," said Erica Meier, executive director of Compassion Over Killing. "It's alarming that this is not only a USDA-inspected facility but a supplier to the USDA."
Online USDA records show the company has contracted to sell ground beef to USDA food programs.
"It's a good sign that the USDA is taking this seriously, but I want to see what comes next," said Meier of Compassion Over Killing, adding the video will be posted on the organization's website.
The case is reminiscent of a 2008 undercover operation by the Humane Society of the United States at the Hallmark slaughter plant in Chino that led to the largest-ever recall of beef and the conviction of two people found to have treated cows cruelly. In that case, video showed downed cows being prodded with a folk lift.
Tracie Cone can be reached at www.twitter.com/TConeAP
The Associated Press contributed to this report.