An inquiry is under way into how a cull of somewhat similar-looking pukeko birds has led to the slaughter of 5% of the wild population of takahē

The head of New Zealand’s national deerstalkers’ association has apologised “to the country at large” after four critically endangered takahē were mistakenly shot by hunters carrying out a cull of a somewhat similar-looking bird.

Deerstalkers were contracted by the Department of Conservation to carry out a cull of pukeko, a non-endangered, very common relative of the takahē, on an island sanctuary in Auckland’s Hauraki Gulf.

Conservation staff discovered four dead takahē, killed by shotgun pellets, on Motutapu Island on 17 August.

The New Zealand Deerstalkers’ Association president, Bill O’Leary, has said he was “quite frankly … appalled” by the error and apologised “to the department and to the country at large”.

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The takahē is a threatened species, native to New Zealand and listed as nationally critical. It was thought to be extinct until a bird was rediscovered in 1948. The conservation department has since invested hundreds of thousands of dollars in rebuilding the population, with its public-private recovery program aiming to establish 125 breeding pairs by 2002.

There are now about 300 birds alive in New Zealand, only between 70 and 80 of which are in the wild. The loss of the four dead birds discovered on Monday amounts to a 5% decrease in the population. It is broadly equivalent to the loss of 160 tigers or 93 pandas.

Before the shootings there were 22 birds on Motutapu Island, one of the conservation department’s predator-free “security sites”.

The cull of pukeko – a native swamphen that is found in vast numbers across the country – was organised because of the damage they cause to the nests and eggs of threatened species. Deerstalkers carried out successful culls on the island in 2012 and 2013.

The department has said that hunters had been carefully briefed on how to differentiate between the species, with takahē about twice the size of pukeko, and flightless. They had also been instructed to only shoot birds on the wing.

The guidelines were introduced seven years ago, after one takahē was mistakenly shot during a pukeko cull on Mana Island, another sanctuary off the Wellington coast.

The Department of Conservation website dispels suggestions that takahē are “just fat pukeko” but concedes the two species look “similar”.

The department has put an immediate halt to the cull as it investigates both its internal processes and the program with the deerstalkers’ association, which it says is “cooperating fully” with its inquiries.