Given the research did not include 2013 figures when more than 60 penguins died at once, Mattern believed the 2060 estimate was optimistic.
"If we don't figure out how we can avoid these mass mortality events, then my gut feeling tells me that the yellow-eyed penguins will be gone by a lot sooner than 2060; so 2040 or 2050."
The population had been falling for some time and the number of breeding pairs on Otago Peninsula had dropped to about 200 from 600 in the 1990s.
Although people in Dunedin and the rest of the south could do little to reverse global climate change, they could push for change when it came to other factors which influenced penguin numbers.
"We can think about how we can mitigate the impact of fisheries, mitigate human disturbance on land and mitigate the impact of predators."
There was no excuse for not acting given the species' economic and cultural significance to Dunedin and New Zealand. The birds greeted visitors to the country on billboards at all major airports, were featured on the $5 note and, according to one estimate, contributed $100 million to Dunedin's economy.
"It's not something we want to lose because we can't be bothered doing something about it."
There was not much data on populations living in the Auckland and Campbell Islands, but it was possible the same trend was happening there also.
The research used 35 years of detailed data collected at Boulder Beach on Otago Peninsula.
It compared the data with sea surface temperature data and it was clear this was the main
environmental influence on penguin numbers.
"However, considering that climate change explains only around a third of the variation in penguin numbers, clearly other factors play a significant role."
It was believed more adult penguins died when the sea was warmer because it meant fewer nutrients from rivers made it to the sea floor, where they fed.
Research by Dr Lance Richdale in the 1940s gave cause for hope.
A warming event in the 1940s meant sea temperatures were increasing, but in the same period yellow-eyed penguin populations were increasing.
Richdale believed this was because World War II meant there was less industrial activity and fishing because so many men were fighting in the war.
Otago University director of wildlife management Phil Seddon said besides highlighting the state of the yellow-eyed penguin, the study also underlined the importance of long-term data sets.
"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, the yellow-eyed penguin,"
Seddon said.
Penguins continued to drown as unintentional bycatch in nets set in penguin foraging areas, suffer from degradation of their marine habitat because of human activities, and died from unidentified toxins.
The authors concluded that "now we all know that yellow-eyed penguins are quietly slipping away we need to make a choice. Without immediate, bold and effective conservation measures, we will lose these penguins from our coasts within our lifetime."
The study has just been published in the international journal PeerJ.
