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Steve Walker, 53, the chair of city's Wildlife Hospital Trust and city councillor Aaron Hawkins have put their names down to take part in the Papatowai Challenge, a 15.5km race in the Catlins next month.
The hoiho - yellow eyed penguin - are the hospital's most frequent visitor, Walker said, with about 105 of the adult breeding population treated over the past year.
While the surgery can be done it comes at a cost - $500 a pop.
They'd set up a givealittle page for people to donate funds with an end goal of about $5000 which would pay for 10 operations.
Speaking to the Herald from a Dunedin pub on Sunday, enjoying a well-earned break after his first runs in more than 30 years, Walker said he didn't realise running would be so taxing on his body.
"I have just genuinely always hated running, I don't really see the point of it unless I'm running away from something."
An avid cyclist and of reasonable fitness, he figured a 5km run would be okay.
"I'm a really keen cyclist and naively said to my friends who are all runners, ah it won't be a problem, I wont need to train because I'm a really good cyclist, an they all just went 'ohhhh'.
"I went for my first training run on Monday and nearly died, actually."
However, he said Hawkins had been in training for a lot longer and looking fit.
Of the injured penguins the said: "It's expensive having them in the hospital. The average cost of them being in hospital is close to $2000 per penguin but the surgery itself is approximately $500. But of course you need the pre stuff and they stay for a week or two weeks depending on their injuries."
One of the board's goals was to make the hospital more financially stability this year.
"The public have really embraced it and Dunedin is doing a fantastic job operationally and I think there's a perception out there that we're honky dory and comfortable but this year will be a big year for us in terms of trying to grab a couple more corporate sponsorships and income via the Government through DoC."
The Natural History of New Zealand had successfully gained funding from NZ On Air to create a five part series of the hospital, an initiative he hoped would give them more publicity and help get more sponsors on board.
The series is due to be aired on Choice TV next summer.
The hospital had also just started taking in yellow-eyed penguin chicks from their nests as they realised they weren't surviving being left by their mothers.
"This year the decision was made to do that, we've had about 15 chicks through the hospital and are in rehabilitation. They simply would have died on the nest so the decision was made to give them a leg up by taking them and hand rearing them."
He said penguins were "robust creatures" and didn't form attachments like some animals, so could be reared and then set free without any issue.