Kea are one of New Zealand's favourite native birds, but they have a vicious side.

The Department of Conservation (DOC) shot a kea that was killing a Queenstown Lakes farmer's sheep.

DOC issued itself and the unnamed farmer two permits to kill the endangered alpine parrot in 2009 and 2011. One kea was shot dead in 2009, according to information contained in an Official Information Act reply.

Both permits were labelled "Authority to destroy absolutely protected wildlife" and show there are exceptions to "absolute protection" – the highest level of wildlife conservation in this country.

Authority for the permit comes from the Wildlife Act, which allows DOC to permit destruction of animals that damage or injure "any stock or crops or ... any chattel or ... other wildlife".

READ MORE: Kea attack sheep in low numbers, study finds

The authority extends to wildlife refuges and closed game areas.

Kea are known to attack and kill sheep, usually by standing on their backs and ripping their loins or backs.

DOC insisted kea had to be "observed on the backs of sheep" and "caught in the act" before they were killed.

According to DOC emails in 2009, the farmer claimed he lost "25-30 sheep in the two months to 9th Oct".

Shortly after, DOC staff saw four marino hoggets had been killed by "kea strike".

The "entire intestinal cavity [was] open" in one carcass. Other sheep survived the attacks but had septic wounds.

Late on October 19, 2009, after the permit was issued, two kea were seen rounding up sheep and a third was on a sheep's back. It was killed.

DOC described the death as a "last resort".

ANDREW WALMSLEY Kea at Arthur's Pass.

Another permit was issued in 2011 but DOC has no records of kea being destroyed under it.

The incident was 'isolated" and "regrettable", Kea Conservation Trust founder and chair Tamsin Orr-Walker said.

The trust was called in to help the farmer in 2010 or 2011, she said. A repellent that makes kea ill was applied to the wool of about 350 sheep and a control group about the same size was also observed.

No sheep died during the experiment, but the trust is not certain the repellent worked due to the limited nature of the trial.

Orr-Walker could not say if farmers were killing kea without a permit, but said she hoped not.

The trust provides free assistance to farmers dealing with kea strike and she urged them to make contact.

In 2011, DOC staff queried internally whether capturing the problem kea and transferring them elsewhere was an option.

The idea was rejected because the birds' chances of survival were unknown and "given the birds ability to travel, it is just transferring the problem".

There is lore in the farming community that kea "ring leaders" attack sheep and other kea then feed on the carcasses.

If the problem individuals are killed, then the problem clears up.

Scientists are less certain about this point, largely because kea strike often happens at night, in high alpine areas, and individual birds are hard to identify.

The Queenstown Lakes District farmer had neighbours whose sheep were also attacked, according to a study published last year.

The neighbours' losses to kea strike were much lower and were viewed as a cost of farming in kea habitat.

The study found about 0.5 per cent of sheep at five South Island high country farms were attacked by kea.

"This study showed that kea strike on sheep was occurring at a low prevalence on the high country farms surveyed."