The National Institute of Water and Atmospheric Research (Niwa) Lauder station specialises in measuring ozone, ultraviolet and greenhouse gas levels.
International organisations and scientists using its data described it as a "global asset" and objected to any job cuts.
Eight international atmospheric organisations, some of them global groups, aired their concerns to Minister for Science and Innovation Steven Joyce last month. One letter was signed by 200 international scientists, who were concerned job cuts would affect the integrity of the data collected.
Niwa's chief scientist of atmospheric research, Dr Murray Poulter, said two jobs would be lost overall and a new position, focusing on atmospheric measurement and analysis, would be created "to help maintain measurement quality and innovation".
Three existing roles highlighted as potential redundancies in Niwa's review of its operation have been disestablished, and one new role created.
Those affected by the job cuts will be able to apply for the new job.
"... Niwa remains committed to supporting its associated facilities and research, which contribute significantly to international atmospheric research and understanding," Dr Poulter said.
"The changes being made will ensure we maintain the appropriate capability to meet the country's science and innovation needs, whilst at the same time using limited resources."
Asked for comment on the job cuts, past president of the New Zealand Association of Scientists and Victoria University Associate Prof James Renwick said he thought the move would be "unpopular", especially with the international scientific community.
"I guess one position retained when three were at risk is better than nothing, but it means there's a pretty skeleton crew now at Lauder."
It was "risky" making the measurement-scientist role effectively a "one-man operation".
There were few atmospheric measurement sites in the southern hemisphere, making the work done by Lauder staff vital on the global stage, he said. "It seems a shame to me that a great arm of the organisation has been pared back to the bare bones."
The cuts were a continuation of "downsizing" that spanned a decade, Assoc Prof Renwick said.
Dr Poulter said the review considered input from within Niwa and from national and international scientists, institutions and programmes.
Niwa would keep supporting Lauder as a key facility and core regular atmospheric measurements there would continue.
Some short-term experimental campaigns would be discontinued to focus on international initiatives, Dr Poulter said.
The planned changes would have a "small impact" on Niwa's ability to conduct internationally recognised atmospheric research and collect core measurements that fed into international work.
The Lauder station celebrated its 50th anniversary last year.
