Disease, the fishing industry, pollution, habitat loss and climate change were having a "much greater impact" on hoiho than being eaten by sea lions, the New Zealand Sea Lion Trust said.
The Department of Conservation said "evidence-based research" would add to the conversation.
Earlier this month, the Otago Daily Times published the views of lifelong fisherman Ken Steel, who said in an opinion piece he had seen sea lions chase and kill hoiho.
"One has to ask, with the marked increase in the fur seal population since the ’60s already reducing the yellow-eyed penguin population via sharing of the inshore food supply, the introduction and breeding encouragement by the Department of Conservation and others of the sea lion population along our eastern seaboard, which has been in the past the principal breeding grounds for yellow-eyed penguins — is it likely to force the extinction of this unique bird?
"Would it not be logical to leave all of our offshore islands to the seals and to protect the habitat and welfare of this unique bird along our eastern seaboard?
"To my mind, this situation is akin to the release of cane toads in Australia.
"In that case, as here and now, everyone failed to see the long-term result."
Yellow-eyed Penguin Trust general manager Anna Campbell said her 3-year-old "could tell you about the food web at sea".
The pressures that led to the danger of hoiho becoming extinct on the mainland were compounding, Mrs Campbell said.
The seabirds were suffering from depleted food sources as a consequence of ocean warming and acidification.
"What is left of the natural food abundance and diversity is under pressure from fishing, which destabilises the climate-stressed food webs.
"On top of that, strong penguins who can cope with the hostile conditions, have been caught in set-nets.
"Deterministic threats that drive extinction must be prioritised. By-catch is a manageable, fully preventable deterministic threat."
NZ Sea Lion Trust co-chairman Shaun McConkey said both sea lions and hoiho had co-existed for thousands of years and could be found doing so on subantarctic islands.
Veterinary experts found diseases like diphtheria, avian malaria and respiratory disease were causing much higher mortality among hoiho than in the past, he said.
"Human effects such as bycatch, pollution, habitat destruction, competition for resources and climate change are having a much greater impact than sea lions.
"Mr Steel's suggestion that we protect the habitat and welfare of hoiho, I assume by the removal of seals and sea lions, would require the culling of hundreds of these native animals.
"To compare the naturally occurring return of an endemic and endangered species (NZ sea lion) to part of its pre-human range, to the introduction of a non-native species — cane toad — by humans is ridiculous."
Doc marine technical adviser Hendrik Schultz said the fisherman’s theory was "interesting" but not what research indicated.
Mainland hoiho were declining due to multiple threats, the vast majority of which were related to humans.
University of Otago marine science researcher Hanna Ravn said a research team had been collecting faeces and vomit from sea lions around Dunedin coastlines since April last year.
"The vast majority of prey are the fish barracouta, jack mackerel and wrasse.
"Interestingly the fish kahawai, which recently arrived from warmer waters up north, is now one of the top preys of choice for our local sea lions.
"The broadness of what pakake [sea lions] eat is quite impressive, with squid and octopus being runner-up to fish, followed by small sharks and skates.
"On some beaches where larger males haul out to rest, we occasionally find evidence of fur seal and penguin in their vomits."
Marine science researcher Dr Chris Lalas said there was evidence the first sea lion born on mainland New Zealand — Mum’s first pup — was killing between 20 to 30 yellow-eyed penguins on the peninsula a year.
Though her behaviour seemed to be highly individualistic, with almost no other sea lions hunting penguins, even if penguins made up "much less than 1%" of a sea lion’s diet if the rare seabirds were to be targeted, it could have an effect on Otago’s small hoiho population.
"It is just individuals doing it and I don't know of any kills happening in recent years," Dr Lalas said.
