Dr Ursula Ellenberg, of the department, said since the mid-1990s the population of yellow-eyed penguins on the peninsula had declined by more than 50 per cent.
"We are effectively losing about 12 breeding pairs per year. If this trend continues unabated, the yellow-eyed penguin might become a rare sight on the peninsula in our lifetimes."
Introduced predators such as stoats, fisheries bycatch and human disturbance were considered the main causes of this overall decline.
"A sudden die-off, like the one we just experienced, significantly adds to the tally."
With about 180 breeding pairs left on the peninsula, about 60 dead adults represented a considerable portion of the remaining breeding stock.
Dr Yolanda van Heezik, also from the department, some of the birds that recently died could have been "super breeders".
They were effectively sustaining the peninsula population, meaning that recovery following their loss could be very slow.
"There are many similarities between 1990 and the current event; the symptoms, localised occurrence and weather patterns. It all points in the same direction and shows that we are dealing with something that might occur again. Only the next event could occur sooner."
Dr Thomas Mattern, who had been studying the penguins' marine ecology, saw strong links between weather conditions and the penguin die-off.
The Department of Conservation biodiversity programme manager, David Agnew, said that finding out the cause of the deaths and being able to predict a recurrence was very important for Doc's management of the penguin species.
With freshly dead penguins available for testing and research already going on in their foraging habitat, researchers here were in a very good position to narrow down the cause, he said.
"Both events were preceded by warm weather which caused unusually high sea surface temperatures. These are ideal conditions for the occurrence of harmful algal blooms and elevated concentrations of toxins."
Considering climate projections were for warmer and drier summers for Dunedin, the penguins might have to cope with similar die-offs more frequently in years to come, he said. Prof Seddon said the economic and tourism importance of the penguins were well documented, with each breeding pair believed to contribute more than $250,000 to the local economy annually.
He would be circulating the funding application in the hope funding for the study could be found quickly.
It could be the case that several organisations would contribute to make the study possible, Prof Seddon said.