Scientists are outraged at proposed cuts to NIWA's world-leading centre in Central Otago which they say is crucial to international research on climate change.
NIWA's atmospheric research station at Lauder, near Ranfurly, has been measuring ozone and greenhouse gases for decades.
Former employee Dr Greg Bodeker says the centre is one of the world's premier sites for atmospheric research.
In the three years since he left, he says, the number of staff has dropped from 16 to 11.
Now three more scientists are set to lose their jobs, which Dr Bodeker says will mean the research programmes will stop.
Dr Bodeker says there is a huge international outcry as hundreds of scientists around the world see this research as critical to their own work.
Former NIWA scientist Dr James Renwick says if three more scientists go there will not be enough people left to do the job, which would damage New Zealand's scientific profile internationally.
"We are a component of a number of these international observing programmes and by pulling back on some of that work we're certainly not pulling our weight internationally in this area."
But NIWA general manager of research Rob Murdoch says the institute is not making any major changes.
He says the organisation is still committed to the internationally significant research at the Lauder centre, just with fewer people.
"We're continuing to collect the same sort of data, it's just that the way we'll be analysing it and the way we'll be modelling it and looking at it has changed focus slightly."
Dr Murdoch says of $40 million in core funding nearly a quarter is still spent on atmospheric and climate research.
The staffing changes are still out for review and a final decision should be made by the end of this month.