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The Wildlife Hospital Trust manager Jordana Whyte said the unexplained respiratory condition affected hoiho (yellow-eyed penguin) chicks across North Otago, Otago and The Catlins.
"We don’t understand how they are getting it and why it is killing them."
On necropsy, it presented as a type of pneumonia.
While a few chicks last year contracted a similar illness, this year the condition was far more prevalent, she said.
It was cause for concern.
"If it gets worse next year, for example, we’ll be in huge trouble."
Concern was strong enough for it to be an all-hands-on-deck situation in resolving it, she said.
Data would be analysed and research conducted into finding any trend.
Diagnosis could not be confirmed until after a chick had died.
"Unfortunately, the chicks that have died will help us figure this out in the end."
The Department of Conservation website states in 1999 there were about 741 breeding pairs in this northern population.
This year, it sat at 167.
Disease was only one challenge to the nationally endangered species.
Others included dogs, human disturbance, climate change, fisheries interactions and predation.
Ms Whyte said the birds did not need any more challenges.
"Even though I can’t draw a line to what’s causing it, the things we know we can change — we have to really ask people to step up in those departments."
Penguin Rescue, based in Moeraki, had an increase in nest numbers this year from 38 to 41.
Sanctuary and Trust manager Rosalie Goldsworthy said it was fantastic, considering the birds were facing possible extinction.
Unexplained chick deaths had always been a problem, and she said stress levels of parents contributed to that.
"It’s very challenging when you’re trying to save a species and you don’t know why they are dying."
She said the survival rate for an individual to reach breeding age was very low.
"That’s the issue, keeping them alive for two years to breed."
She said it was always good to know why things were dying.