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The discovery was made by Niwa climate scientists and glaciologists last month, during the annual long-term aerial Snowline Survey of the South Island's glaciers.
Niwa scientists take to the skies every March to record the snowline altitude of up to 50 glaciers, using specialised cameras from a light aircraft.
Thousands of photos are taken from different angles to build 3-D models of glaciers that can be compared year on year, to give an accurate depiction of how much of the previous winter's snow remains to contribute to long-term glacial ice accumulation.
The information gathered over the past four decades has produced a unique and valuable data set that provides an independent measure of how climate change and variability are affecting New Zealand's water resources.
Although Niwa scientists are still piecing together data from the latest survey, project leader Andrew Lorrey said it was not hard to miss the fact that some of the smaller glaciers at lower altitudes had now disappeared.
"It's really sad to see that some of our smaller glaciers - particularly on the fringes of the Southern Alps, that are a little bit lower in altitude like North Canterbury and as you go south out of Queenstown - are reducing to nothing.
"There's no reason for me to go to Caroline Peak [near Lake Hauroko] anymore.
"There used to be a snow patch and glacier on the spine of that peak, and based on what we saw last year, there was no real reason for us to go back there this year. There probably wouldn't have been much of anything left there."
He said a glacier on Mt Wilson in North Canterbury was also gone.
"It's now down to two very small snow packs, or remnant glacial pieces, that are like the size of a couple of dining room tables.
"It's looking pretty grim.
"One of the pilots said, `There's no need to come back here anymore'. And he's right.
"There's not really anything we can tell from those glaciers anymore because they're gone."
Dr Lorrey said it was the sad reality of the changing climate of the region.
"For anyone who says global warming is a farce, I would say let's have this conversation in front of a disappearing glacier in New Zealand.
"It's very hard to argue against physical evidence like this, where these glaciers are so acutely attuned to what's going on with temperature.
"The fact that they are disappearing, and they are largely driven by fluctuations in our temperature, speaks volumes about what's going on."