He warned that the fur seal population was booming, and said that unless drastic measures were taken the penguins could become extinct on the island and the nearby Fleurieu Peninsula.
"The beanbags are simply Kevlar bags full of lead shot, and they're discharged from a shotgun," he told the ABC. "It hits the seals like a punch and it will not penetrate the skin provided it's fired from sensible distances. Now seals are very smart and they move away from an area if they've been disturbed."
Conservationists, however, are opposed to such tactics, and the state Environment Department said this week that "interactions between New Zealand fur seals and penguins are a natural phenomenon over which humans have little control".
It said the seals, a protected species, were only now recovering from commercial sealing in the late 18th and early 19th centuries. The penguins are not endangered.
Sealing - Australia's first major industry after colonisation - nearly eradicated the fur seal, with an estimated 100,000 animals killed in South Australia alone. Although it was banned in the 1830s, until 1983 fishermen were allowed to kill seals deemed to be "interfering with fishing operations".
In recent decades the Kangaroo Island population has bounced back to about 25,000 - and the number of penguins has declined in tandem, claim tourism operators.
Simone Somerfield told the Australian last year that visitors to her penguin viewing centre at Penneshaw had seen the birds being ambushed by seals in the shallows and even chased on to the shore.
"Every now and again you would see one penguin being taken, and I would say 'Gee, that's amazing, it's like David Attenborough'," she said. "But then it was more and more and more, and then mass kills in which the seals were not even eating them. It was happening within 100m and you have a complete view - it was like watching a horror movie."
Seal numbers are believed to have increased partly because of a decline in numbers of sharks and killer whales, their natural predators. In the past, there have been demands - supported by the fishing industry - for some of Kangaroo Island's fur seals to be culled, sterilised or relocated.
Ayliffe, who maintains that penguin viewing is important to the island's economy, said: "The increase in New Zealand fur seals has led to the rapid decline of penguin numbers in the area because the New Zealand fur seals are eating them."
"Harvesting" of seals was carried out in South Africa, Namibia and the Northern Hemisphere because there was not enough food for the increasing seal numbers, he said.
"Harvesting is a major tool used internationally to manage numbers. It's only a matter of time before we implement some control measures here in SA ... to ensure tourism assets stay viable."
At Cape Gantheaume, a protected wilderness area on Kangaroo Island, there used to be a thriving fairy penguin population, Ayliffe said.
"The New Zealand fur seals started breeding there and ate all the penguins. Eventually the penguin will become locally extinct around Kangaroo Island and the southern Fleurieu [Peninsula] area."
But environment officials have rejected measures such as culling and relocation, saying they have proved expensive and largely ineffective when tried elsewhere.
New seals move into areas from which others have been removed, and relocated seals swim long distances to return to familiar feeding grounds.
Moreover, penguins form only a small part of the fur seal's diet, according to marine biologists.
