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Yellow-eyed Penguin Trust general manager Sue Murray called the deaths at the trust's Long Point Irahuka Reserve south of Owaka ''devastating'' in so far as they were ''totally preventable''.
Signs at the reserve clearly indicated dogs were not allowed.
The South Island's estimated 250 breeding pairs of the bird remain the lowest for one of the world's rarest penguin species for more than a quarter of a century, and experts have predicted the penguins' extinction from mainland New Zealand because of threats such as climate change, starvation and disease, including avian diphtheria and avian malaria.
When the trust bought the reserve in 2009, 48 breeding pairs of yellow-eyed penguins called Long Point home.
At the start of this latest breeding season there were 18.
Necropsies performed at Massey University had now confirmed both birds died from wounds consistent with dog attacks.
During a check on moulting penguins at the reserve south of Owaka early this month, trust ranger Ben Goldsworthy discovered the body of the second bird - a ''bloody and recently-killed hoiho'' - with dog tracks nearby.
The trust ''can't afford to lose any more to dog attacks'', he said.
Department of Conservation Murihiku operations manager Tony Preston said dog owners were required by law to ''ensure their dog does not injure, or cause distress to wildlife''.
Early this year a dog killed a Snares crested penguin on the beach near Kakanui.