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University of Otago zoology researcher Dr Thomas Mattern oversaw the creation of a model two years ago which assessed the decline of the species and estimated hoiho would be gone from the mainland by 2060.
However, after two extremely poor breeding seasons, the outlook was even more dire, he said.
"I give them another decade."
At this rate, they would be "functionally extinct" by then, which would mean although there could still be some individuals around, the population would not recover.
That was down from 261 two years earlier.
Conservation Minister Eugenie Sage at the weekend released a draft recovery strategy for the species along with a five-year action plan, created with Ngai Tahu, the Yellow-eyed Penguin Trust and Fisheries New Zealand.
It promised an extra $220,000 over three years towards the animal's conservation.
Dr Mattern said there was "a lot to take in" within the strategy.
He hoped in the future, more focus would be placed on marine threats to the birds, which had been neglected in the past.
This involved rising sea temperatures, food shortages and set netting.
"It's a topic no-one really wants to touch."
The strategy promised to "turn around the fortunes" of the endangered animal, but Dr Mattern said he "had his doubts" about this on the mainland.
The next hope were populations on the subantarctic islands, the numbers of which were largely unknown, which were not exposed to mainland threats such as dogs and set nets.
Penguin Place manager Lisa King said Dr Mattern's numbers were "probably quite right".
The centre had 304 individual birds through its rehabilitation centre last season, out of a total estimated mainland population of 700.
Its recent average was 100 "patients" annually.
"The population is in big trouble. It is depressing, but there's only so much you can do."
The strategy was left "far too late", she said.
"We'll need a lot of luck."
Penguin Place rehab manager Megan Abbott said while there were a range of reasons for the penguins coming to the facility, the most common was starvation.
She would not be surprised if the drop in breeding pairs for the next season was "fairly steep".
Yellow-eyed Penguin Trust executive officer Sue Murray said it recognised Dr Mattern's work and the importance of marine threats, but other matters such as disease also needed to be addressed with urgency.
It had not done similar modelling so could not comment specifically on his findings.
Conservation efforts had "not stopped", she said.
The trust was putting more resources into the Catlins, Stewart Island and its own reserves for early disease management with the involvement of its scientists.
The trust believed the recovery strategy went far enough, but public feedback would help to establish whether others agreed.
It was the first time Fisheries New Zealand was involved to such an extent, she said.
"I think it's a result of a true partnership at work."
Ms Sage said she was "seriously concerned" about the decline in the mainland population of hoiho and Dr Mattern's research highlighted the urgency of the work needed.
"That’s why public feedback and making this plan as strong as possible is important.
"The strategy highlights that the immediate focus must be on the survival of individual hoiho to ensure we have a future population. This means continuing with management interventions such as caring for sick, injured and underweight birds."
She agreed more emphasis needed to be put on reducing marine threats.
Hoiho were a priority for the department and her personally, Ms Sage said.
She was discussing with the department whether more funds would help or whether other issues such as tackling marine threats was a higher priority.
"I want to repeat my thanks to all the experts and volunteers who are doing they can to support the species."