Stewart Island has just been officially declared a breeding colony for one of New Zealand's most treasured and critically endangered species.

But the success of New Zealand sea lions on Rakiura doesn't change the fact the species is under huge pressure and producing 1500 fewer pups than two decades ago, says a Massey University scientist helping carry out the monitoring.

The annual count in Stewart Island has revealed 55 pups this season, and now that the numbers have been consistent for several years, it can be declared a breeding colony.

"A new breeding colony is huge news for New Zealand sea lions," Department of Conservation (DoC) marine science advisor Laura Boren said.

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"Sea lions have been showing signs of recolonising on the mainland, but it has been slow going."

The remote and forested habitat at Stewart Island's Port Pegasus had provided a safe stepping stone for sea lions to increase in numbers.

"This is great for the species as, if this colony continues to grow, it provides more resilience to disease and storms in the overall population.

"It may also help facilitate recolonisation on the Otago and Catlins coastline or elsewhere on the mainland."

DoC's Rakiura senior biodiversity ranger Kevin Carter said pups had been counted annually on the island for the past eight years.

"The past couple of years has seen a real increase in search efforts – we know more about their behaviours and where they hang out," Carter said.

"It's possible this group reached breeding colony status some time ago, however until we had the numbers for this year we could not say for certain.

A sea lion at Stewart Island greets a group that stopped off there during a 2014 conservation expedition to the subantarctic islands. Photo / File
A sea lion at Stewart Island greets a group that stopped off there during a 2014 conservation expedition to the subantarctic islands. Photo / File

"Either way, the future of the Rakiura population is looking positive."

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But Associate Professor Louise Chilvers, of Massey's School of Veterinary Science, said the bigger picture was less positive.

"It's fantastic that it looks like they are establishing a colony down there, but it's small and it still needs protection to really grow and become a functioning part of the population for the species."

Chilvers, who has long been doing the annual count with DoC, said that less than 20 years ago, about 3000 pups were born on the species' stronghold on the subantarctic Auckland Islands every year.

"At the moment, we have just over 1500 being born - so it's almost as if 1500 aren't being born anymore."

She said it was fortunate that their habitat on the lower half of Stewart Island was relatively unpopulated, and had few visitors.

"Last year there was a proposal to establish a fish farm down there - that's been stopped, but things like that could have a major impact on such a small population."

Conservation Minister Eugenie Sage acknowledged more work needed to be done to protect the species.

Pegasus Bay in Stewart Island. Photo / File
Pegasus Bay in Stewart Island. Photo / File

"New Zealand sea lions face a range of threats from disease to commercial fishing and deliberate attacks by humans," she said.

"With the population at just 12,000, their future relies on the actions we take now to protect them and their habitat."

Last year, the Government released a five-year Threat Management Plan - a programme of engagement, targeted research, direct mitigation, and regular monitoring at all known breeding sites.

Since then, researchers have been at Auckland Islands studying Klebsiella pneumonia, a bacterial disease potentially killing large numbers of sea lion pups.

At Campbell Island researchers in collaboration with Deep Water Group have been seeking solutions to the high mortality caused by pups getting trapped in coastal holes.