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The young kaki (black stilt), one of only 132 adults remaining in the wild, went under the knife at the Wildlife Hospital Dunedin.
The native wading bird from the Mackenzie Basin sustained severe foot injuries requiring treatment with antibiotics and painkillers, followed by surgery to repair the damage.
"Hopefully he will get out in the wild again, but they have a potential captive plan if not.
"He's got quite good genetics, so... if he can't be released and needs to be monitored, they (the Department of Conservation) will be able to incorporate him into the breeding programme.''
One of New Zealand's leading wildlife surgeons, Dr Argilla said it was a privilege to work with the precious species, nearly as rare as kakapo in the wild, but the stakes were high.
"There's always pressure, it doesn't matter what species it is. He's critically endangered so that puts more pressure on... because every bird counts when they're critically endangered.''
Her previous work with similar foot injuries on yellow-eyed penguins had informed Dr Argilla's approach for the kaki.
"The infection has destroyed the bones in his toes, so there's no hope of him ever having a bone in his toe, which is really sad.
"There's two options we could have gone for - option one, which is the easier option, would have been to just amputate the toes, which leaves him with two toes on each foot,'' she explained.
However, the wildlife hospital staff were unsure how the formerly three-toed bird would cope in the wild with just two, as this could fatally compromise his balance.
Staff decided the best approach would be to remove the infected tissue and pieces of bone and leave some tendon and soft tissue behind to scar.
"And you leave a decent-sized stump and hopefully that provides a weight-bearing surface that he can walk on.''
The lively black bird was anesthetized about 10.30am today.
In August 2017, he was released in the Tasman Valley, one of about 130 that year.
Dr Argilla said the valley was intensively trapped by Doc, which has improved the survival rate of kaki and other braided river nesting birds.