The allegations were made by animal rights group Animal Equality after it released video footage showing pigs being kicked, slapped and attacked with iron bars at a Norfolk farm.
Stephen Brown, who runs the 4,000 pig unit at Harling Farm, in East Harling, near Norwich, said he was co-operating with investigators.
“We are horrified to learn of what has allegedly happened and have dealt with the staff involved appropriately,” he told a reporter from the BBC.
“We are co-operating fully with all investigations and are pleased that the RSPCA has visited.
“We take animal welfare extremely seriously and place it at the heart of everything we do here.”
An RSPCA statement said that it had received the footage on Friday 10 February.
“The RSPCA was disgusted by the apparent deliberate animal cruelty being inflicted in the footage, which has been reviewed by one of our farm animals scientists,” the statement said.
“It is one of the worst cases of animal abuse we have seen.
“Within hours of receiving the footage on 10 February 2012 two RSPCA inspectors and a chief inspector attended the farm to check the welfare of any animals there.
“We are treating this matter extremely seriously and a full and thorough investigation has begun.
“As with any other RSPCA investigation, if evidence of deliberate cruelty and/or suffering in contravention to the Animal Welfare Act is found, a file will be passed to our prosecutions department to determine whether or not to start legal proceedings.
“While the investigation continues it is not appropriate for us to make further comment as it could jeopardise a possible future prosecution,” the statement added.
Animal rights organisation Animal Equality said that the investigation marked the beginning of an intensive campaign “to expose the true face of animal farming in Britain”.
“It provides a stark contrast to the pig industry’s celebrity-endorsed ‘Love Pork’ marketing campaign,” said a spokeswoman for the group.
It said the footage was filmed by an undercover reporter between 27 July and 30 September last year.
Meanwhile David Clarke, the chief executive of Assured Food Standards which operates the Red Tractor scheme, condemned the behaviour on the farm.
“The behaviour shown on the video had no place within the assurance scheme and we completely condemn it.
“As soon as we were alerted to the issue on Friday of last week, we immediately removed the farm from the scheme on the basis of the video evidence and we have had an inspector on the farm during the weekend.”
He added: “We are reviewing our systems in light of the lessons learned here and will almost certainly revert to more unannounced inspections.”
Commenting on the Haling Farm case, Zoe Davies National Pig Association general manager said:
“Any kind of cruelty is completely unacceptable. But what is disgusting, is that this footage was taken between July and September last year and they (Animal Equality) have waited until now to release the footage and to make a point about the Red Tractor, for whatever reason that may be.
“This in itself is disgusting and they should have taken it straight to the RSPCA. This does not reflect normal practice in the pig industry.”
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