Last updated 12/02/2013
Officials are hoping the die-off does not become as bad as that of 1990 when almost 150 adult penguins died.
Department of Conservation (DOC) officer David Agnew said it took the penguin population in the area several years to recover from that event.
It was hoped the deaths were being caused by a biotoxin occurring naturally in the marine environment, and for now it was assumed the fish the penguins were eating was making them ill.
"We're hoping that whatever is causing it, perhaps weather conditions affecting the water column, will dissipate so the penguins will return to normal, and hopefully penguin adults will stop dying," Agnew said.
The first dead penguin was found on January 21, and the most-recent were found on the weekend, although some of the latest birds had been dead for some time.
"It's quite a blow," he said.
"In some cases both the male and female of a pair might have succumbed to this."
Agnew, who is DOC's programme manager for biodiversity assets in coastal Otago, said DOC staff were surveying more beaches today.
The dead birds had been sent to Massey University for autopsies. All had been found to have been in good condition when they died, without any obvious cause of death.
Two birds that had died recently were being sent to the Cawthron Institute to be tested for toxins. It was hoped to have the results of those tests by early next week, Agnew said.
As well as the impact on the penguin population, another issue was that the birds were important for some tourism businesses.
He noted that the 40 deaths were spread over 13 breeding sites, so people visiting the sites were still able to see penguins.
As in the 1990 event, dead birds were only being found around the Otago Peninsula, while penguins in North and South Otago were unaffected, Agnew said.
Altogether there were about 450 to 500 breeding pairs of the penguins around the South Island coast.
The timing was different in 1990, when the penguins started dying earlier, meaning many more chicks had to be taken into captivity, where they had to be looked after for much longer.
He said that was not such a big issue this time as the young birds were due to head out to sea about mid-February. This summer had been good for chicks, with the young birds mostly reaching good healthy weights. Any that were found to need help, perhaps underweight or with both parents dead, were being cared for.
"For us it's the loss of the breeding adults. They know how to survive, where to forage and where to breed," Agnew said.
A plan was being prepared to ensure as rapid a recovery as possible of the yellow-eyed penguin population on the peninsula.
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