Many chicks were struck down by illness: avian diphtheria, an infection that causes ulcers to form in penguin chicks' mouths making it difficult to eat and breathe, has hit all chicks at some breeding sites.
Some chicks had died due to high heat, as they remained under the protection of their parent's body. "We've lost about 50 chicks, despite our more intensive efforts this season," said Coastal Otago Biodiversity Ranger Mel Young.
Ailing penguins were given salmon smoothies every few days, and had the lesions in their mouths removed allowing them to eat and breathe easier. Despite such efforts, about 45 per cent of chicks at monitored sites had died. "There's no obvious pattern to the outbreak of infection, but most chicks that have been infected have also been underweight. We can't be sure if illness or starvation has driven the observed mortality, but the heat certainly has played a large part too."
Tourists visiting sites had caused problems. The Department of Conservation urged visitors to take established tours, rather than explore on their own, so as not to disturb breeding sites.
It was a sentiment echoed by the Yellow-eyed penguin trust, which said visitors should take regulated tours. "The penguins seem to have had a tough four breeding seasons, so we're just trying to minimise every possible thing we can to give them their best chance of survival," said general manager Sue Murray. "I think it's just been a bad run. There are other birds out there that are just not breeding, so we're hoping they're just having a year off and we'll see them back again next year."
Penguin rehabilitation centres, including Penguin Place, were preparing for a busy season.
The facility is funded through guided conservation tours, and has taken in hundreds of sick penguins in the last few years.
Manager Lisa King said every year a new problem seemed to afflict the region's penguins. "There's lots and lots of different reasons... each year it has been a different issue."
In recent years, barracuda maulings, starvation, and orphaned chicks abandoned by their parents had resulted in visits to the Penguin Place by troubled penguins.
Penguins are subject to many dangers, which have resulted in a falling population.
Alongside disease, dangers include interference from humans and livestock at breeding areas, heat stress, predation by stoats and ferrets, and dog attacks, which have reduced the number of chicks in recent years.
In 2013, a mass mortality event, believed to be a toxic agent, killed around 70 adult and juvenile penguins on the Otago Peninsula. Later that year, low food supply had left penguins emaciated and unable to moult without intervention. Earlier this year, around 55 penguins were maimed in suspected barracuda attacks.