An investigation was launched after animal rights campaigners shot undercover video of Scotpigs' Ormiston unit near Kirknewton.
Quality Meat Scotland says it has now withdrawn permission from the piggery to sell its produce as "farm assured".
One of Scotland's leading food safety experts, Professor Hugh Pennington of Aberdeen University, said the possibility of serious infection was a grave concern.
He was commenting after seeing pictures which the pressure group Advocates for Animals claims to have taken inside Ormiston Farm, near Kirknewton in West Lothian.
The farm is run by Scotpigs - a company set up in 1998 by north-east pig farmer Arthur Simmers.
Mr Simmers was not available to speak to BBC Scotland at his farm complex at Whiterashes in Aberdeenshire - but Scotpigs financial controller Donald Repper said the accusations came as a bolt out of the blue to him.
Mr Repper said Scotpigs had started their own investigation and would make no further comment.
Pictures condemned
Advocates for Animals described the scenes they videoed at Ormiston Farm as "horrific".
Director Les Ward said: "Our video shows horrific scenes of pig cannibalism, a sea of rats swarming over pigs' bodies, and pigs knees-deep in their own excrement.
"The public rarely gets to see the reality of what goes on behind the closed doors of factory farms in the ever-increasing effort to produce cheap meat.
"Our findings must raise serious concerns about intensive pig farms across Scotland and the rest of the UK."
Professor Pennington said: "Over recent years people who grow pigs have learned that biosecurity - that is keeping out bugs - is extremely important.
"And what we are seeing here is just the opposite of that."
Following an inspection of the farm, a spokeswoman for the Scottish Society for the Prevention of Cruelty to Animals said there were no welfare concerns for the animals but there were "serious problems" with pest control and the building that housed the animals.
Pest problem
She said: "Today the inspectors saw 17,000 animals. Some of the pigs were dirty but there were no animal welfare concerns.
"Some of the animals have been suffering an illness but we know they have received veterinary treatment since January 24.
"What is unacceptable is the state of the building and the number of the rats, which are over-running the place.
"The video shows a dead pig being eaten by another pig but that is symptomatic of animal behaviour.
More checks
She said the vets and the SSPCA would make further examinations but there were no grounds to prosecute on welfare concerns.
She said the group would be putting pressure on the farm's owners to control the pest problem as quickly as possible.
A Scottish Executive spokesman confirmed that State Veterinary Service inspectors had been at the farm but could not comment on their findings before they had presented their report.