Half the usual number of yellow-eyed penguins are expected to take their first swim this year from the usually productive Long Point breeding area in the Catlins.
Department of Conservation coastal Otago ranger Mel Young said 52 eggs were laid, 38 hatched and 35 chicks were seen at 80 to 90 days of age at Long Point. Only 28 chicks are thought to be healthy enough to fledge this year at roughly the 105-day mark.
Past research shows mortality rates soar after fledging, she said.
''On average, there's an 81% mortality rate in that juvenile year - so you're not expecting 28, you're expecting four or five to survive.''
Last year, 60 penguin chicks fledged at Long Point, while 71 fledged in 2013.
Yellow-eyed Penguin Trust general manager Sue Murray said she was not ready to call the poor season for fledgings a crisis, but the trust was worried about the breeding season in what had been a good breeding area.
The next breeding season in spring would be important for the birds.
''This is the third poor breeding season in general that yellow-eyed penguins have experienced. It is only the first poor season in the Catlins.
''The fact that it is now more widely spread is of concern to us,'' she said.
''There's always natural fluctuations in a population, so we hope this is just one of those natural dips. It's when we get a dip for two, three, four years in a row - that's when we start getting concerned.
''We have that concern about the birds on the Otago Peninsula. As yet, we don't have the same level of concern for the Catlins - but on saying that, the numbers were extremely low everywhere, right across the geographical range this year.''
A deadly disease that affects up to 90% of chicks has plagued penguin populations at Otago Peninsula since 1999 and is still not well understood.
It is hoped testing from a study undertaken by Doc and the Ministry for Primary Industries late last year will produce a trial treatment for what is being called avian diptheria that could be ready for next spring.
But so far the disease, which causes lesions in chicks' mouths and makes eating and breathing difficult, has not seemed to affect the Catlins birds.
''There is avian diptheria there, but it doesn't seem to affect the population to quite the same extent as it does on the Otago Peninsula - and we don't know why that is either,'' Mrs Murray said.
However, this year, Ms Young said monitoring teams did not see any sign of the disease in the Catlins chicks.
Despite a record number of barracouta attacks and an unexplained mass death of adult penguins at Otago Peninsula two years ago, Ms Young was optimistic about the birds' future at Long Point, saying penguins ''don't breed every year just because we want them to''.
''If the conditions are poor for breeding, they should be making that decision for themselves.''
Ms Young said 30% to 40% of breeding adults in the Catlins had a ''year off'' breeding.
Egg laying and hatching were the latest ever recorded and breeding had been delayed for the past three seasons in a row throughout coastal Otago.
''For some birds, having the year off means they're hitting the reset button. We're hoping there will be early egg laying next season,'' she said.
This past season there were 29 nests at Long Point.
While the number was low, it fitted within the range recorded over the past 10 years of monitoring. From 2005 to 2014, the nest numbers had ranged from 25 to 53 nests, Ms Young said.
''I'm optimistic next season will be better. Beach counts in the Catlins by volunteers showed more than twice the number of adults returning home compared to the nests known at some key sites.''
