The country's largest privately-owned conservation project has been allowed to show off kiwi to wealthy tourists without a permit.
Complaints to the Department of Conservation (DOC) accuse the Cape Sanctuary at Hawke's Bay or putting tourist dollars ahead of kiwi health.
It comes as a report of the spotted kiwi two summers ago reveals they died from neglect.
A video of Sir Paul McCartney cuddling a squirming kiwi during a visit to Cape Sanctuary in December 2017 has been viewed more than 466,000 times.
But DOC admits the ex-Beatle should not have been allowed to hold the bird because only kiwi handlers can do so.
Furthermore, the sanctuary did not permit the kiwi advocacy tours, meaning it was in breach of the Wildlife Act.
The sanctuary thought it was DOC thought it did too, DOC Hawke's Bay operations manager Connie Norgate said.
"It has not been anybody in particular's fault and certainly not Cape Sanctuary, more so DOC."
She was not used for advocacy, especially in Sir Paul McCartney's case.
"Internationally that probably got some good coverage for the plight of kiwi, which is a really cool thing.
"When we put it into context, kiwi is out there every day on public land where there is not any management or pest control."
It was not until she started investigating complaints made in January 2017 that she realized it did not have a permit.
Those complaints, obtained by RNZ under the Official Information Act, included concerns about high turnover of staff, the death of two kaka in cat traps in October 2017 and the death of nine Little Spotted kiwi in 2017.
There were also companies that provided kiwi tours to paying guests "took precedence about other higher priority kiwi management".
The choice of birds used for tours was "guided by convenience rather than absolute requirement for health check" and the tours were done at the expense of pest control in the little spotted kiwi sanctuary.
DOC finally issued Cape Sanctuary a 10-year permit on the 27 August, a few weeks after RNZ began making inquiries.
The Cape Sanctuary is situated on Cape Kidnappers, on three properties owned by American billionaire Julian Robertson and the Hawke's Bay Lowe and Hansen families.
It's not open to the public but at Mr Robertson's $ 2000-a-night Farm at Cape Kidnappers hotel can pay another $ 600 to accompany sanctuary staff carrying out health checks on kiwis.
RNZ understood these tours were often held when guests demanded them, even if it meant kiwis were handled more than they should.
Former Maungatautari Restoration Project kiwi manager Matthew Lark said the practice of kiwi tours was a contentious issue in the conservation community but the fault lay squarely with DOC.
"There is a generic culture in many North Island sanctuaries that many people are not allowed to do, but many are not inspected by the department."
Concerns that kiwi tours at the Cape came at the cost of other species were lodged with DOC in October last year. That was after nine little spotted kiwi left between sometime between November 2006 and May 2017.
RNZ has been told at least 15 birds died – or nearly half the population – but they were not officially recorded because not all birds were radio tagged.
A report into the deaths, by Steve Sawyer and RNZ, admitted radio monitoring of the birds was irregular between late 2016 and early 2017.
"At the same time the level of predator control at this site was not expected to be high-standard, and it is important that we have adequate protection for little spotted kiwi."
The owners of Cape Sanctuary were unavailable to comment on the little spotted kiwi, or the unpermitted tours, and related questions to Mr. Sawyer.