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Niwa's annual end-of-summer survey of the snowline on key South Island glaciers showed they lost much more ice than they gained between April 2008 and March 2009.
Scientists flew over 50 glaciers in the Southern Alps and Kaikoura area and photographed the positions of snowlines on glaciers during the survey.
Niwa snow and ice scientist Jordy Hendrikx said above-normal temperatures, near or below-normal rainfall and above-normal sunshine were among the reasons for the continued shrinking.
This year's snowline was, on average, 95 metres above where it needed to be to keep the ice mass constant, Niwa said.
This indicated the loss of glacier mass observed in the 2007-2008 survey had continued.
Over the past 33 years, there had been an overall decrease in the glacier mass balance, despite periods where the balance had increased for a few years.