The penguins face extinction by 2060, a new study suggests.

One of the world's rarest penguins is under threat of extinction, Otago researchers say.

In parts of the coastal South Island habitat, yellow-eyed penguin breeding grounds have fallen silent and only "the odd lonely pair" of penguins cling to survival.

The nationally endangered species, the hoiho, could disappear from its Otago habitat by 2060, according to new research.

SUPPLIED The penguins are classified as nationally endangered.

University of Otago zoologist Dr Thomas Mattern said the study used forecast climate change models to predict the impact on penguin populations.

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Yellow-eyed penguins' habitat ranges across the southeast South Island, Banks Peninsula, Stewart Island, and Auckland, Campbell, and Codfish islands.

IAIN MCGREGOR/FAIRFAX NZ Yellow eyed penguins at Katiki Point near Moeraki in Otago.

He said their predictions were conservative and did not include sudden shocks to the penguin population such as a "die-off" in 2013 when more than 60 penguins died.

Every year since then has been a poor season for breeding.

"Any further losses of yellow-eyed penguins will bring forward the date of their local extinction.

Mattern said the birds, which feature on billboards in airports and on the NZ$5 note, were widely recognised.

"Yet despite being celebrated in this way, the species has been slowly slipping towards local extinction."

Increasing sea surface temperatures partly explained the negative trend in penguin numbers.

"The problem is that we lack data to examine the extent of human impacts, ranging from fisheries, introduced predators to human disturbance, all of which contribute to the penguins' demise.

"However, considering that climate change explains only around a third of the variation in penguin numbers, clearly those other factors play a significant role. Unlike climate change, these factors could be managed on a regional scale," he said.

Dr Ursula Ellenberg, who has studied the penguins for more than 10 years, said the breeding grounds were now silent.

"It is sobering to see the previously busy penguin-breeding areas now overgrown and silent, with only the odd lonely pair hanging on," she said.

University of Otago director of wildlife management Professor Phil Seddon said the long-term study of penguin breeding was made possible by long-term data collection.

"In the current era of fast science, long-term projects have become a rarity.

"Without more than 35 years' worth of penguin monitoring data we would probably be still at a loss as to what is happening to a national icon," he said.

The authors concluded that without 'immediate, bold and effective conservation measures" the penguins face extinction "within our lifetime".

The study was published in the international journal PeerJ.

According to the researchers' prediction models, the breeding success of the penguins will continue to decline to extinction by 2060 largely due to rising ocean temperatures.

The chances of seeing the penguins in the wild are quietly slipping away, the research said.