This is a glimpse inside a Victorian caged hen farm approved by government inspectors less than six weeks ago.

Photos taken at the Yarra Valley farm in March show dimly lit sheds with bald and dead chickens, including a hen, surrounded by fresh eggs, decomposing at the bottom of a cage. One chicken removed from the farm had half its body weight in pus drained due to an infection.

The images, according to the activists who broke into Wagner's Poultry Farm in Coldstream, provide a reality check of caged chicken factories.

But the owner of the 6000-bird farm that sells caged, free-range chicken and duck eggs has denied claims that the animals were mistreated, and said he was satisfied all birds were being cared for properly.

Hans Wagner, who has run the farm for 50 years, said he met all regulatory requirements, adhered to the industry's code of practice and had never been prosecuted for animal welfare offences. "The authorities come out here and there's no problem," he said.

The government department responsible for animal welfare in commercial facilities confirmed two recent inspections did not find any breaches under animal cruelty laws.

But activists from Animal Liberation Victoria said they found birds living in appalling conditions - in the two weeks after government health officials last inspected the farm - and removed several hens in need of veterinary care from cages.

"It was filthy dirty," vice-president Patty Mark said. "We found sick and deformed hens left to die in cages. They were debilitated and exhausted, had severe feather loss and red-raw skin."

Avian vet Corrie Pinkster, from the Melbourne Bird Veterinary Clinic, said she was hired by the activists to examine one of the chickens before it underwent surgery for an oviduct infection, a common condition affecting laying hens.

"We actually removed 1.2 kilograms of pus from a bird that weighs 2.3 kilograms, so it was literally half her body weight," Dr Pinkster said.

"It was a severe case. It would have been pretty obvious she wasn't in a good state and there's no way she would have been laying eggs at that point."

Mr Wagner said staff swept the sheds daily and that while the dead birds shown in the images should have been removed immediately "mistakes are made sometimes".

"Lots of things can kill chooks," he said. "I'm not going to say how many we lose a day, [but] it's not very many. There's always problems, we're talking about livestock."

Mr Wagner, who has scaled down the operation from a 50,000-bird farm, said he bought thousands of chickens at a time and was unable to inspect them individually.

He said feather loss was common among older laying hens as their stores depleted, and that it was not a sign of animal cruelty or poor living conditions.

Chickens can also lose feathers for other reasons, such as pecking from other birds.

Mr Wagner said he had filed a complaint with police about activists trespassing on his property and stealing chickens. "They don't like chooks in cages, basically that's what I have," he said. "They come here, they take pictures allegedly, as far as I'm concerned they could have even brought the birds with them."

Animal welfare officers from the resources department gave Mr Wagner's farm the all-clear in December 2014 and late February. It is understood the farm was directed to make minor improvements to address concerns about conditions inside the sheds.

Agriculture Minister Jaala Pulford's office said staff would visit the property again in April to assess the health and welfare of the chickens.

Concerns about employee safety at the farm were also raised after the workplace watchdog received a complaint from activists about a large gap in the floor of one of the sheds, and cabling across walkways.

WorkSafe said inspectors had visited the farm last week and identified a number of safety issues. "Interim measures have been put in place to ensure the health and safety of farm employees until the issues are resolved," a spokesman said.

The RSPCA said the photos from Wagner's Poultry Farm highlighted the "extensive animal welfare problems" in cage systems. "It's time that these cruel and outdated systems be replaced with cage-free facilities," a spokeswoman said.