The Food Standards Agency and the RSPCA have launched investigations into an abattoir after undercover footage revealed shocking abuse and neglect of horses.

The footage also shows allegedly illegal procedures when slaughtering horses destined for European food markets. Two slaughtermen have had their licences withdrawn as a result, the food watchdog said.

The film was taken at the Red Lion abattoir near Nantwich, Cheshire, after an eight-week investigation by the Hillside Animal Sanctuary.

It comes amid public anger that some of the biggest supermarket chains, including Tesco, have been selling beefburgers and other products containing horse meat.

The abattoir footage shows horses being beaten with sticks, a rope or an iron rod to encourage them into pens. Some are crammed into the slaughter pens in pairs and on one occasion in a group of three, and are then stunned together.

Under the Welfare of Animals Regulations 1995, horses should not be slaughtered in sight of one another because of the distress it causes.

Craig Kirby, FSA head of approvals and veterinary advice, said: "I was shocked by the footage and that is why we took immediate action to make sure the individuals involved could not continue to slaughter animals. The FSA takes animal welfare at slaughter very seriously, and we will always investigate and take action when we see breaches of the legislation."

The FSA is investigating further with a view to a potential prosecution.

Wendy Valentine, founder of Hillside Animal Sanctuary, described conditions at the abattoir as "really traumatic".

"It was just so harrowing and horrifying," she added.

An RSPCA spokesman said: "The footage is shocking and upsetting to watch. With the Welfare of Animals (Slaughter or Killing) Regulations 1995 in mind, we have concerns that horses appear to be in the stunning pen at the same time rather than individually, as the law requires.

"We also have concerns about some of the animals that appear to be injured. We have requested a copy of the unedited footage with a view to investigating."

Red Lion told Sky News that it treats animal welfare and public health with paramount importance.

"In attendance at the Red Lion abattoir are three full-time food standards officers comprising of an official veterinarian and full-time meat hygiene inspectors throughout production," it said in a statement.

The incidents in the footage are "not the norm but of an isolated nature", it added.

The abattoir said it has taken disciplinary action against the individual featured.

Its statement said: "I agree horses should individually enter the stunning area and most certainly not three at a time. However, small horses and ponies having spent years together as companions are difficult to separate. Horse lovers would understand that.

"My opinion and that of other veterinarians is it is better to keep those types together to reduce the stress, providing swift dispatch is achieved."

The abattoir said its meat was not part of the recent supermarket burger scandal.