Department of Conservation staff are working tirelessly to find out what has killed four kākāpō chicks and an adult bird this month.
The death of the four chicks including three within three days of each other leaves only 74 chicks in the breeding programme. There are 144 adult birds also in the programme.
Dr Andrew Digby tweeted that it was "troubled times for everyone involved as we try to understand what's caused the recent spate of aspergillosis in chicks and adults".
Tests have confirmed that several of the chicks have died from aspergillosis - a respiratory problem caused by fungus.
They have been carrying out CT scans at Auckland Zoo on some of the chicks and an adult kākāpō to help diagnose the cause.
Blood tests are also being carried out at Whenua Hou and some birds whose results reveal high white blood cell counts have been flown to Auckland Zoo for treatment.
Adult kākāpō Gumboots died last weekend after apparently getting his leg trapped in the fork of a branch.
"The loss of Gumboots is a particularly bad blow as he was a founder who'd had no offspring. He was found as an adult on Rakiura in 1988," Digby tweeted.
Then within a few days of each other chicks Waikawa-4-B, Bella-2-A and Tumeke-4-A and Queenie-4-A-19 also died.