Swinbanks described the University of Otago as a "leader" in tectonic research.
"Proximity to Antarctica has also led to New Zealand's impressive performance in climate science, work that Victoria University of Wellington has been at the forefront of for decades."
Data for the University of Auckland showed it excelled in the life sciences, including drug discovery and bio-engineering.
New Zealand's top 10 also includes four research institutes: GNS Science (fourth), the National Institute of Water and Atmospheric Research (seventh), AgResearch (ninth) and Malaghan Institute of Medical Research (10th).
University of Canterbury is fifth and Massey University is sixth, and Callaghan Innovation, a government agency supporting high-tech business, was eighth.
Science and Innovation Minister Steven Joyce said the result was a "great endorsement" of the quality of New Zealand's scientific research.
"New Zealand research and researchers are very well-cited and acknowledged around the world as first class, and not just in the physical sciences area."
The upcoming Statement of Science Performance will go into this in more detail, he said.