Kea are native parrots that forage for food in the forest and around human settlements.
The kea deaths have sparked a recommendation in an internal Department of Conservation (Doc) draft report that the 1080 poison-drop programme be reviewed.
Doc monitored 29 kea - 17 at Franz-Fox, 10 at Haast and two at Hohonu - for two months after aerial 1080 drops during 2007 and 2008.
None of the kea monitored at Haast and Hohonu died during the monitoring period, according to the Doc report.
The report says "aerial 1080 may well be a significant threat to the kea population".
It also concludes "some 1080 operations are probably devastating, while others may be neutral or beneficial."
Anti-1080 poison campaigners have seized on the report as support for their argument that compound 1080 (sodium monofluoroacetate) devastates native bird populations and has chronic effects on other species.
But Doc says more research is needed to accurately measure the impacts of 1080.
Pre-feed was sown over the entire area of the Franz-Fox and Hohonu drops but over less than 50% of the Haast area.
The report suggests future research address three questions: whether kea that have never eaten "junk food", or human food waste, are less vulnerable to 1080 poisoning; whether using less toxic bait reduces kea kills without compromising possum kills; and whether pre-feeding increases kea kills.
Doc radio tagged and monitored kea at various sites during the poison programme and monitored them regularly for two months afterwards.
Six Franz-Fox birds died within three weeks of poison sowing and subsequent lab tests on the carcasses showed 1080 was the likely cause of death.
Three birds had directly consumed the bait.
Three other kea had empty stomachs, but it was assumed the birds died of direct bait consumption.
The seventh kea gave a mortality signal after 36 days, but the transmitter and carcass have not been recovered.
It has been assumed it also died of 1080 poisoning.
The report has called for more research to better quantify the risk to kea and how to minimise it.
It was hypothesized the high death rate at Franz-Fox may have been because juvenile kea in the area had a habit of investigating "human-type" junk foods.
Kevin O'Connor, DOC's general manager of research and development, said in a media release the draft report was yet to be independently peer reviewed.
More research was needed to ensure the effect of 1080 on kea was well understood and that the benefits outweighed the potential risks, he said.
"The recommendations from the preliminary report call for larger samples of radio-tagged kea to be monitored through aerial 1080 operations from areas away from waste dumps and road-end car parks where kea have never eaten junk food.
This has already begun.
"The recommendations also call for a review of the strength of the toxin in some aerial operations and a review of the use of pre-feed in some instances.
"Pre-feeding with non-toxic baits has improved the quality of pest control when toxic feed is applied.
"With methodical application of scientific principles, the long-term costs and benefits of aerial 1080 use in kea habitat can be quantified," Mr O'Connor said.
Anti-1080 poison protesters have long argued 1080 causes unacceptable collateral damage to other species and should not be used to kill possums.
Paul Murray, the spokesman for Karameans Advocating Kahurangi Action (Kaka), said in a media release this week the recent kea deaths clearly showed the "devastating impact the 1080 programme is having on native bird populations nationwide".
Mr Murray said 1080 poison could also cause chronic effects in other species such as infertility and birth defects.
Doc's $1.7 million aerial 1080 programme during 2007 and 2008 sparked angry protests from West Coast residents.
The poison was dropped in the Arawhata and Waipara Valleys, the Western Kahurangi Valley, the Whakapohai and Thomas Valleys, the Copland Valley and at Whataroa.
The largest mission ever undertaken in New Zealand was in January, in the Arawhata Valley, near Haast, where 109 tonnes of cereal bait was dropped by 13 helicopters in one day.
Possums were the main target of the programme, but the poison also killed other pests such as stoats, rats and ferrets.
The possum population is rampant on the West Coast, where they eat native trees and prey on native birds and eggs.
Aerial 1080 has been used in kea habitat for about 50 years to reduce the impacts of high densities of possums.
About one-eighth of Docs' $13 million pest control budget is allocated to possum control over 1 million ha nationwide.
