A bird cull on a New Zealand island has been halted after marksmen killed four rare takahe, an endangered species with only 300 known to exist, officials said.

The deaths were "deeply disappointing", Conservation Department director Andrew Baucke said in a statement.

He said "experienced members" of the local deerstalkers association were undertaking the cull, targeting the over-populated pukeko on the island sanctuary of Motutapu near Auckland.

"The hunters had been carefully briefed on how to differentiate between the flightless takahe and pukeko, including instructions to only shoot birds on the wing," Baucke said.

An examination of the four dead takahe showed they were killed by shotgun pellets.

Of the 300 takahe known to exist, there were 21 at the Motutapu sanctuary where the aggressive pukeko numbers more than 1,000 and is considered a threat to the rare species.

Deerstalkers Association president Bill O'Leary told Radio New Zealand he was "appalled" by the accidental deaths.

"We're very conscious of the fact that the birds are an endangered species and that was the purpose of the cull on pukekos because of the damage that they do to nests and to eggs."

The takahe were thought to be extinct until their rediscovery in southwestern New Zealand in 1948.