A scientist says it's possible several kākāpō have died because of a mystery disease, known as crusty bum.
There are estimated just to be 154 of the rare species in the country.
Andrew Digby is the science adviser for the Department of Conservation's kākāpō recovery programme.
He said so far the disease had been confined to birds on Codfish Island, west of Stewart Island.
Dr Digby said it was still unclear what caused the disease.
"We had this big explosion last year and we're really trying to get to the bottom of it, so we've got several research streams going on to try and understand it.
"Because we just don't know what it is yet, we don't know if it's a virus, we don't know if it's a bacteria, we don't know if it's something like an immune system response, so it's a puzzle and it's a problem, it's a big management problem for us."
But Dr Digby said it had been a great breeding season for kākāpō with 32 surviving chicks this season.
He said it was also the first time that there had ever been kākāpō breeding on three islands.