The Deerstalkers Association has apologised after some of its members shot four protected takahe during a pukeko cull on Motutapu Island.

The hunters, contracted by the Department of Conservation, shot the endangered birds by mistake on the Hauraki Gulf island sanctuary.

Deerstalkers' Association President Bill O'Leary said he is appalled, and he is apologising to DOC and the country at large.

O'Leary said the Deerstalkers Association is committed to working with DOC to protect endangered species and back country assets.

He hopes the mistake doesn't impact that relationship.

Volunteers are used to cull pukeko on Motutapu Island because the birds are aggressive and prey on the chicks and eggs of high-risk populations.

However, Doc has put an immediate stop to the culling of pukeko in areas where there are endangered takahe.

DOC's Andrew Baucke said it's not the first incident of its kind, and the department has launched two inquiries in response to the latest shooting.

"One's an internal one to look at our own policies and processes around the cull programme and one's an external one to also look at the programme with the Deerstalkers."

The mistake has angered Iwi, who approved the transfer of the rare birds from the South Island earlier this year.

The country spends tens of thousands of dollars a year on takahe preservation.