The allegations - which made the front page of The Independent today (18 June) - came following an 'major investigation' by vegan group Animal Aid.
During "unannounced" visits to farms in Cornwall, Somerset, Lincolnshire, North Yorkshire and East Riding of Yorkshire in March and April 2008, the group claims to have shot photos and footage of "dead, dying, sick and injured pigs, existing in filthy, cramped conditions."
Animal Aid specifically targeted farms belonging to industry leaders - two had board members of BPEX as their company directors and others were connected to the National Pig Association (NPA), the Pig Industry Development Scheme, the European Pig Producers' Association, the NFU and the Farm Animal Welfare Council (FAWC).
The group has criticised the industry's 'Save the British Pig Farmer' media campaign, claiming that the images of healthy pigs used on promotional advertisements do not reflect British pig farms.
Animal Aid head of campaigns Kate Fowler-Reeves said: "The pig farming industry has recently launched a media offensive to persuade the public that they should buy British because of the exceptionally high welfare standards on British pig farms. But rarely has there been such a huge disparity between marketing hype and truth.
"While the idealised vision is perpetuated through expensive PR offensives, and while 'celebrity' farmers plead for the future of 'high welfare' pig farms, the wretched truth is pushed aside: that welfare standards on typical British pig farms are abysmally poor."
The industry has been quick to respond to the allegations, and BPEX has already commissioned inspections of the farms involved.
A BPEX spokesperson said: "We are concerned that allegations of cruelty should be made against British pig farms. We have obtained the names and addresses of the farms involved and have commissioned independent inspections as a matter of urgency, as provided for under farm assurance schemes which underpin the Quality Standard Mark.
"British pig farmers are justifiably proud of their welfare standards, which are among the highest in Europe. We will be contacting Animal Aid to discuss the matter further once the results of the independent inspections are known."
Pig farmers maintain that their welfare standards are excellent, and say they have nothing to hide.
Meryl Ward - one of the BPEX board members singled out by the investigation - today invited press to have a look around her farm, emphasising the confidence British pig farmers have in their welfare standards.
"We take these sorts of allegations very seriously, but all the farmers I have spoken to are entirely confident that their standards are above board, and are more then welcome to open their doors to the relevant authorities to come and have a look at them," said NPA general manager Barney Kay.
There have been questions raised about the potential biosecurity implications of Animal Aid's investigations, and the NPA has urged any farmers who suspect a break-in by Animal Aid or any other welfare group to contact them, so that they can report it to the relevant police department.
Kay said: "It is extremely concerning that people are illegally entering farms unannounced and then potentially going on to other farms.
"We have no idea what farms they went from and to. They could be transferring disease from one farm to another, which could cause animal health and welfare problems."