She said Countdown was being targeted because its parent company, Woolworths Australia, plans to end the practice from 2018.
"It makes sense: if they did it in Australia, why not here?"
She said it was distressing to see hens caged. "They spend their lives in a cage, the day they get out is the day they die."
Countdown's general manager of merchandise, Chris Fisher, said the situation in Australia was not comparable to New Zealand.
"Woolworths Australia's pledge was made within a market with a different supply chain and under a different regulatory environment."
Countdown offered customers a choice between free range, barn and cage eggs. "In this respect we are no different to other major retailers."
Antoinette Laird, the head of external relations for Foodstuffs, which manages Pak'nSave and New World, said the poultry industry did not have enough capacity to supply exclusively non-cage eggs, given customer demand.
"We believe it's important to maintain the affordability of an important dietary product such as eggs to all consumers."
Skilton said it was disappointing that it came down to money. "It's disheartening to see animals treated that way just for money."