The programme had been dealt a blow with the discovery of dead kakapo Barnard by kakapo rangers on Codfish Island, near Stewart Island, last weekend, programme manager Deidre Vercoe Scott said yesterday.
Rangers had been looking for him on Codfish Island, also called Whenua Hou Island, for his annual transmitter change.
The recovery team was "pretty gutted", especially since the death appeared to have gone unnoticed for up to three months, Ms Vercoe Scott said.
Barnard was discovered on Stewart Island in 1982. His age was unknown.
He had since fathered eight chicks, including five of the 11 hatched during the last breeding season in 2011. His death reduces New Zealand's overall kakapo population to 125.
In the past 12 months, six of the critically-endangered flightless parrots have died, the largest number of deaths in a 12-month period since the internationally respected recovery programme began in 1990, organisers said.
In predator-free surroundings, mature kakapo have a high survival rate, and deaths have averaged no more than about three a year since 1990.
Programme staff sighted the birds only once a year for health checks and a transmitter change, but prided themselves on having technology that "allows us to monitor our precious population, with minimal interference," Ms Vercoe Scott said.
Tracking technology was constantly changing to increase the information that could be collected and there could have been "some problems" in interpreting the complex transmitter signals accurately.
This would be closely investigated because identifying a "mortality signal" more quickly meant better information could be gained from a subsequent autopsy.
Team members were upset but "not alarmed" by the recent deaths, and there was no "pattern" suggesting one main cause, she said.
The six deaths involved birds ranging from juvenile to mature and causes of death also ranged widely, including disease and an accident involving a bird which was snagged by its transmitter harness on Anchor Island, in Dusky Sound, Fiordland.
The programme's overall "huge positivity" should not be forgotten - given the total kakapo population had risen from 49 in 1990 to 131 last year.
Nevertheless, the recent deaths were a reminder kakapo were still critically endangered and, given an ageing population, an increase in mortality was inevitable.
But more than half the population consisted of young breeding-age birds and there were indications there would be a breeding season this summer.
University of Otago zoologist Dr Bruce Robertson said it was "very comforting" overall kakapo numbers had continued to grow since 1990, and juvenile birds were adding to the population.
