Horrifying undercover footage from inside a Californian slaughterhouse shows incompetent workers standing on the mouth and nostrils of a cow to suffocate it after failing to kill the animal with a bolt-gun.

The shocking video, which allegedly demonstrates rampant animal abuse and suffering from inside Central Valley Meat Co., has led the the U.S. Department of Agriculture to shut down the slaughterhouse which was a major supplier of their National School Lunch Program and In-N-Out Burger.

The sad film produced by animal rights group Compassion Over Killing reveals how already sick cows are stunned when they are unable to walk to their deaths and shows how they are hoisted up by their legs onto conveyor-belts even if the bolt-gun has failed to kill the animal.

A cow starts vomiting after a pneumatic bolt gun fails to kill it as it is transported along a conveyor belt in a slaughterhouse

Most of the animals slaughtered by CVM are 'spent' dairy cows who are no longer economically viable as milk-producers to the dairy industry.

And now USDA regulators who shut down the slaughterhouse after viewing the animal welfare video are investigating whether beef from sick cows reached the human food supply.

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.

There is no indication any of the cows slaughtered at the Central Valley Meat plant were diseased and the USDA did not order a recall of beef coming from the plant.

A spokesman for In-N-Out Burger said that CVM provided between 20 to 30 percent of the meat used by their restaurants and that it canceled its contract immediately.

The west cost burger chain has a loyal following and is regulalry patronised by Hollywood celebrities such as the soccer player David Beckham.

On the firm's website the chain claims to make its own hamburger patties 'using premium cattle selected especially for In-N-Out Burger', and says it pays 'a premium' for this.

In a statement to ABC News, the company's chief operating officer, Mark Taylor said, 'In-N-Out Burger would never condone the inhumane treatment of animals, and, in fact, all of our suppliers must agree to abide by our strict standards for the humane treatment of cattle.'

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 (COK).

The footage shows animals bleeding and thrashing after being repeatedly shot in the head with a pneumatic gun in unsuccessful efforts to kill them 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.

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.'

Another cow bleeds profusely from its nose after a bolt gun fails to kill it at Central Valley Meat Co. in California

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.

In the four minute video compiled by the animal rights group various abuses towards the cows are witnessed.

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 kill it.

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.

After viewing the video, famed Californian fast-food firm In-N-Out Burger immediately severed their ties with CVM.

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.