The Farm Transparency Project has accused workers at the export company, MD Foods Australia, of killing sheep and goats without fully stunning the animals.
Project director Chris Delforce also accused the workers of roughly handling the stock in video recordings made in April.
Mr Delforce acknowledged the project had committed trespass to install the cameras.
Victorian Agriculture Minister Ros Spence said there was no tolerance for animal cruelty, and her department was working with the Commonwealth to investigate the matter.
Agriculture Victoria was advised on Wednesday, August 14, that a formal complaint had been submitted about a facility in Echuca.
The Echuca abattoir is a Commonwealth-registered facility, but the welfare of livestock in Victoria is protected under the Prevention of Cruelty to Animals Act.
Agriculture Victoria officers enforce this legislation.
Mr Delforce said most people would be “shocked and horrified” to see the footage.
“Right now, Victoria is discussing new animal protection laws which acknowledge for the first time that animals are living, feeling, sentient beings,” he said.
“We cannot accept this while simultaneously turning a blind eye to the suffering of millions of animals in Australian farms and slaughterhouses.
“If our government were serious about animal welfare they would shut these places down for good.”
Farm Transparency Project informed the abattoir of what it was doing on August 13.
“We’ve reported this facility to the relevant authorities, as we have for the other 17 slaughterhouses we have exposed since March last year,” Mr Delforce said.
MD Foods Australia could not be contacted.