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Forest and Bird have been helping the tītī - also known as muttonbird or sooty shearwater - breed at Sandymount for the past two seasons.
But a ferret slipped through the trapline in April, killing the monitored chicks just weeks before they were due to fledge.
Forest and Bird volunteer and contractor Graeme Loh said it was a gruesome scene to find.
"Each burrow still had the body of a large plump fluffy chick, dead from injuries to the neck," he said.
"After months of work, one ferret had got through the trapline and wiped out the entire colony. It was a massacre."
Forest & Bird confirmed volunteers would be shoring up predator control on the clifftop site ahead of this breeding season.
The seabirds returned three weeks late, while other colonies were reporting fewer numbers arriving from the northern hemisphere.
"Nowadays there are a few remnant mainland colonies, which are in desperate need of protection," Ms Cunninghame said.
"Otago would once have supported several million breeding tītī - sooty shearwater - and it would be great to see them return in large numbers. But to do this we must make the sites where they can breed free of predators, in addition to addressing the threats seabirds face at sea.
"We are securing funding to extend our predator control in the area and will also be using a conservation dog and cameras to help identify and monitor the burrows after the birds lay eggs in early December."
While Ms Cunninghame said the predator work only focused on a fraction of the bird's life, it was a vital time.
"After they fledge, all we can do is wish tītī good luck and hope that, against all odds, they'll someday return to Sandymount to have chicks of their own."