Despite the video being handed to the regulator earlier this year, Star Poultry Supply abattoir was permitted to continue operating.
The secretly-recorded video shows hens flapping their wings as they are dipped into boiling water, designed to strip them of their feathers.
Animal rights activists have used similar tactics to draw attention to the conditions of chickens kept in cages, prompting many consumers concerned about animal welfare to switch to buying free range eggs.
But animal rights activist Tamara Kenneally, who helped record the abattoir footage, said many hens die like this regardless of whether they are cage, barn or free range.
"I do want people who eat eggs to watch it just to know what's happening to those girls," she told the ABC's 7.30.
Chickens are killed when they reach the end of their egg-laying lifespan at about 18 months old.
Under industry regulations, they should be stunned then killed by having their throats slit.
The regulator was given the footage from the Keysborough abbatoir in March of this year.
In a statement, Victoria's abattoir regulatory body PrimeSafe said an investigation led to some remedial action, including changes to staff.
"The business was subject to enforcement action and increased regulatory oversight until improvements in animal handling, including back-up slaughter, were implemented."
Star Poultry has not responded to SBS News' phone calls.
