Traces of the rat poison, Brodifacoum, have been found in two little blue penguins that died in the Hauraki Gulf, a month after the Department of Conservation dropped the poison on Rangitoto and Motutapu islands.
Tests on five penguins recovered from Auckland's Long Bay beach found two had traces of the poison in their livers - but at levels too low to have killed them.
Vets at Auckland Zoo found the birds probably starved to death, which DoC said was not uncommon for penguins in winter.
However, poison-drop project manager Richard Griffiths said the finding of Brodifacoum was "alarming" and DoC did not know how it had happened.
Tests on penguins and dolphins were commissioned partly to ease public speculation the poison was linked to the recent deaths of dogs, dolphins, penguins and fish in the Hauraki Gulf.
The deaths of several seemingly healthy and well-fed common dolphins remain unexplained, after tests on their livers and stomach contents showed no traces of either Brodifacoum or tetrotodoxin - the toxin found found to have killed five dogs in July and August.
Mr Griffiths said the penguin finding was unexpected.
"It is a surprise because we've never had penguins dying at the same time as pest eradication [operations] before, so we've never had reason to test them."
The three aerial drops of 147 tonnes of poison-laced cereal bait - the last on August 7 - were part of a project to create a sanctuary for rare birds.
Zoo vets found the dead penguins were thin, had empty stomachs and showed no signs of internal bleeding - the major symptom of death by Brodifacoum.
Mr Griffiths said it was possible they ate pellets out of desperation.
"We don't have any idea about how they might have come across Brodifacoum, but I guess it is important to note that they were hungry - they were starving penguins - so they may have eaten a bait."
Pilchards taken from the dolphins' stomachs and dolphin livers tested negative for Brodifacoum, as did shellfish taken from around Rangitoto and Motutapu after the poison drops.
DoC's resource consent to drop Brodifacoum on Rangitoto and Motutapu envisaged that some of the poisoned cereal baits would end up in the sea, and fishermen reported seeing pellets fall into the ocean at the time.
A summary Mr Griffiths wrote ahead of the drops said that a maximum of 1288kg of bait would fall into the ocean around the joined islands' 56km coastline.
That was much less than the 18,000kg of Brodifacoum-laced baits that spilled into the sea near Kaikoura after a truck crash in 2001 - which contaminated shellfish within a wide area.
Auckland Regional Council commissioners, who approved the operation, found the risk to marine creatures was low because the poison was not very soluble in water, and the cereal pellets broke down within a few hours.
Meanwhile, DoC has asked algae specialists at the Cawthron Institute to test dead dolphins for domoic acid, an algal toxin known to kill dolphins, and results were expected this week.
Rat poison discovered in dead penguins
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