"It's very difficult to deal with," he said.
South Island iwi Ngai Tahu are understood to be angry about the deaths, and Mr O'Leary said he had been considering how best to approach the iwi to offer an apology.
"We haven't had a chance at this stage, we've certainly been thinking about how we approach that."
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 needlessly been bowled over by some deerhunters is just really disappointing."
His party colleague and conservation spokeswoman Ruth Dyson described the shooting as "wanton destruction".
"It appears the culling was completely unsupervised given the dead takahe were found some time after they were shot. And it isn't the first time this has happened," she said.
"Is the Department of Conservation so poorly resourced that it can't even supervise such culls?
"To have taxpayers money spent on killing endangered birds is disgraceful and deserves a full explanation."
The pukeko cull was undertaken by "experienced members" of the local deerstalkers association, DoC's northern conservation services director Andrew Baucke said.
DoC was in talks with the association, which is said to be "co-operating fully" with inquiries.
Mr Baucke said takahe and pukeko had similar colouring and could be mistaken for each other.
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."
Mr Baucke said the deaths were "deeply disappointing" for DoC and the volunteers. All culling operations had been put on hold while a review took place.
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.
Pukekos are as common as 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.
Takahe facts
• 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 facts
• 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
Source: Department of Conservation
- With additional reporting from NZME News Service
