At the centre of the concerns is the welfare of a 26-year-old South Island kākā recently transferred from the Te Anau Bird Sanctuary to Dunedin.
Veterinarian Dr Christina Abramowicz, of Aongatete in the Western Bay of Plenty, complained to the Department of Conservation (Doc) and the Ministry for Primary Industries (MPI) after last week visiting the aviary where the native parrot is housed.
This week, MPI said it was "looking into" her complaint.
Doc said the bird needed more time to settle in after the move.
Dr Abramowicz said she saw the bird, known by Dr Abramowicz and her former Te Anau keepers as "Charlie Girl", hanging upside down from her enclosure "weaving" and obsessively grooming her feet.
The weaving behaviour Dr Abramowicz compared to a child clutching their arms together, keeping their head down and rocking back and forth in an attempt to soothe themselves.
It indicated a "high level of stress".
"Multiple" kākā at the Dunedin aviary displayed behaviour that suggested their mental wellbeing was not being looked after, she said.
Kākā were highly social, highly intelligent animals and other birds would respond to a "stressed environment", she said.
"You can’t ‘settle in’ from distress, you need the support, you need a proper assessment and acknowledgement the stress is there.
"You need a proper treatment plan."
A Dunedin City Council spokesman said the Dunedin Botanic Garden aviary was an accredited operation with appropriately trained staff.
The council had "no concerns" about the operation there, he said.
Doc South Island kākā breed for release programme technical adviser Bruce McKinlay said the department took claims of bird welfare extremely seriously, but a check at the aviary last week showed nothing of concern.
"By all previous accounts Charlie has been settling in well and engaging with other birds and being stimulated by their company.
"She has only been there for a month, and it’s not unexpected for there to be a settling in period.
"The breeding programme has been incredibly successful making a real difference for wild populations of kākā," he said.
MPI compliance and response director Glen Burrell said MPI received a complaint from Dr Abramowicz on July 17 "and we are looking into it".
Veterinarians for Animal Welfare Aotearoa managing director Dr Helen Beattie said in New Zealand there were not a lot of vets who could provide expert behavioural assessment, "no matter what species you’re talking about".
