The hunters were carefully briefed on how to tell the difference between them, including instructions to only shoot birds on the wing, he said.
"Guidelines introduced after an incident on Mana Island seven years ago when another takahe was mistakenly shot during a pukeko cull were also used during last week's cull."
The embarrassing mistake has angered iwi who approved the transfer of the rare birds from the South Island to the sanctuary.
Despite long-running conservation efforts, there are only 300 takahe left and the species is classified as "critically endangered".
The takahe on Motutapu had been translocated from the Fiordland National Park, where the only wild population of the birds is based.
South Island iwi Ngai Tahu are understood to be angry about the deaths, especially as it came soon after the recent controversy in Southland about the hunting of keruru, another protected species.
Labour MP Rino Tirakatene, who had spoken to Ngai Tahu conservation board members, said: "There's no way that they would send their treasured takahe to a sanctuary for it to be slaughtered.
"There are even calls for the return home of those birds. There is a lot of goodwill that goes with these gifts to improve the biodiversity and to see that they've been needlessly been bowled over by some deerhunters is just really disappointing.
"It shows complete incompetence on DOC's part to bring in these Barry Crump-type good keen men."
Pukekos are as common and ducks and geese and because they are a highly aggressive species they are considered a threat to rare native bird species.
Takahe were thought to be extinct in the early 20th century but were rediscovered in 1948 in the South Island. Two-thirds of the population are now based in "safe sites" including Motutapu, while around 100 live in the wild within Fiordland National Park.
DOC, in partnership with Mitre 10, has a goal of establishing 125 breeding pairs by 2020. The public-private conservation programme has been running for 11 years at a cost of $292,000 to DOC and $150,000 to Mitre 10.
President of the Deerstalkers' Association Bill O'Leary said he accepted that a DOC investigation will determine that the birds were killed by a member or members of the association.
"I share with the department a concern that the deaths will affect efforts to save an endangered species.
"I apologise to the department and to the country at large.
"The NZDA is committed to working with the department to protect endangered species and back country assets. I trust that this tragic incident will not harm the generally positive relationship we have with the Department of Conservation."
Takahe
Population: 275-300
Habitat: Fiordland National Park (wild). Maud, Mana, Kapiti, Tiritiri Matangi and Motutapu islands (sanctuaries).
Appearance: Dark blue head and neck, turqouise and green back and wings, red beak and legs.
Adult size: 50cm long, up to 3kg
Pukeko
Population: Abundant
Habitat: Marshy roadsides and low-lying open country throughout New Zealand.
Appearance: Deep blue colour, with black head, red bill and legs.
Adult size: 50cm long, 1 to 1.5kg
- Department of Conservation
- With additional reporting from NZME News Service
