The farmers believe the DPI broke its own animal welfare standards when testing pigs for the virus at Cosgrove earlier this year.

The President of the Victorian Farmers Federation's pig group, John Bourke, says the DPI did not allow its own specialised pig vet to be part of quarantine process.

"To exclude a well-known veterinarian and having another qualified vet that has no pig experience, he's wandering around in the dark," Mr Bourke says.

"Hopefully, this won't happen again."

The DPI deputy chief vet, Dr Andrew Cameron, says the department's vets are well trained, and he had been unaware until now of the pig farmers' concerns.