A new sea lion breeding colony has been declared on Stewart Island, the first on mainland New Zealand for more than 150 years.

New Zealand's critically endangered sea lions have taken so well to a remote Stewart Island spot, they have been declared a breeding colony.

The annual pup count revealed 55 new sea lions were born this season at Port Pegasus, a remote spot on the southern tip of the island.

Numbers have been consistent for several years, meaning it is now officially a breeding colony, the first new such site on the mainland for more than 150 years.

SUPPLIED Researchers counted 55 new pups this season at Port Pegasus, a remote site in the south of Stewart Island.

Louise Chilvers, an associate professor at Massey University who helped carry out the count, said it was "very exciting" news.

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"New Zealand sea lions used to breed from Cape Reinga all the way down to the subantarctic [islands], but at the turn of last century they mostly got wiped out during the sealing age.

KELLY BUCKLE/MPI New Zealand sea lions are at grave risk of extinction, with a population of about 12,000 in Otago, Southland and New Zealand's subantarctic islands.

"For them to come back and start breeding again is fantastic."

The New Zealand sea lion/rāpoka is a taonga species, treasured by tangata whenua.

Thought to be the world's rarest sea lion, it is endemic to New Zealand and with numbers hovering around 12,000 is regarded as nationally critical, the highest level of threat and at grave risk of extinction.

RICHARD COSGROVE Environmentalists hope the Port Pegasus colony will provide a stepping-stone to help sea lion numbers increase.

With sea lions being slow-breeding and long-lived, Chilvers said the addition of 55 pups is significant given that females give birth only once every few years after reaching maturity at the age of five.

And while the new colony is no safeguard for the species, she said it is a step in the right direction.

"It is a phenomenally good thing, but still in the last 15 to 20 years the population down on the Auckland Islands has dropped by almost half.

"So 55 pups on Stewart Island doesn't make up for almost 1500 pups that are no longer being born down in the subantarctics.

"But we know there are problems going on down in that population, so having a new population that's starting away from whatever those problems are is a really good thing. As long as we can hopefully protect them they should grow."

Sea lion pup counts on Stewart Island have taken place annually for the last eight years, with concerted efforts to find new young in the last few seasons.

Conservation Minister Eugenie Sage welcomed the news of the new colony, but said more work was needed to protect sea lions and their habitats from disease, commercial fishing and deliberate attacks by people.

Laura Boren, a marine science adviser at DOC, said the new colony was "huge news".

"If this colony continues to grow, it provides more resilience to disease and storm events in the overall population.

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

Last year the government unveiled a five-year plan to carry out intensive research and monitoring at all known sea lion breeding sites, leading to the study of a disease thought to be responsible for large numbers of pup deaths on the Auckland Islands and researchers working to prevent pups dying from falling into holes and becoming trapped on Campbell Island.