The court backed the science that led the National Institute of Water and Atmospheric Research (Niwa) to conclude that New Zealand's climate warmed almost 1°C between 1909 and 2009.
New Zealand Climate Science Education Trust, a private body that rejects the argument that human activity has caused global warming, went to court alleging Niwa's methodology was flawed and its findings were not peer reviewed.
Judge Geoffrey Venning rejected the allegations in a written ruling handed down on Friday, saying Niwa acted "in accordance with internationally recognised and credible scientific methodology".
"The plaintiff does not succeed on any of its challenges... the application for judicial review is dismissed and judgment entered for the defendant," he wrote.
Venning ordered the trust to pay Niwa's costs.
Niwa was not immediately available for comment but a group of six climate change scientists from New Zealand tertiary institutions including Wellington's Victoria University and the University of Otago welcomed the decision.
"The basic science of climate change has been established for well over a century, and almost all scientists active in climate research agree that human activity is causing the climate to change," they said in a statement.
"For a small group of scientists to appeal to a court of law to find otherwise is bizarre."
They said climate change had caused glaciers to retreat in New Zealand over the past century, as well as rising sea-levels globally and a reduction in arctic sea ice.
"This misguided action of a small group adds confusion to a simple issue - the world is warming and future generations of New Zealanders will have to deal with the consequences," they added.