The station near Lauder has become one of only four certified sites in the Global Reference Upper Air Network (Gruan), a climate-monitoring network - and the only certified southern hemisphere site.
Two other sites exist in the southern hemisphere, and 10 in the northern, but they are not certified.
Gruan is run by the World Meteorological Organisation.
Niwa atmospheric scientist Dr Richard Querel said the recognition of work done at the Lauder site, which has a 54-year history, was ''great''.
Accurate observations were crucial to documenting climate and climate change.
''It's nice to be formally recognised for the work we do. Sometimes the work can seem a bit hidden, since we make these high-quality measurements and then submit them to a far-off database for other scientists to use.
''It also helps a lot in our communications with our funders - mostly the New Zealand Government - and the New Zealand public as a whole.''
The site is already renowned in the international scientific community for its work.
Benefits from certification would likely come in the form of collaborations with other organisations, he said.
Not only was the Lauder site the best-equipped in the southern hemisphere, but its location added to its value.
''Lauder is located at 45 degrees south. This latitude is almost completely ocean, so Lauder measurements are representative of a large fraction of the earth's surface not covered by any other ground-based measurements.''
The remote, relatively untouched atmosphere was also a long way from areas heavily influenced by human development, he said.
An event at the Lauder site in early March will mark its certification.
