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The New Zealand Association of Scientists last night also jointly awarded the Marsden Medal to Prof Mick Clout, of Auckland University, for ''important contributions to conservation ecology''.
Prof Hunter was a ''recognised leader and innovator in environmental and chemical oceanography'', award officials said.
''His research is characterised by the application of fundamental chemistry to the investigation of the oceans, in all their complexity,'' officials said.
The Marsden Medal acknowledges a lifetime of outstanding service to science.
Prof Hunter is the Otago pro-vice chancellor, sciences, and co-director of the collaborative Niwa-Otago University Centre for Chemical and Physical Oceanography.
In 2011, the centre won the $500,000 top award in the Prime Minister's science prizes.
Prof Hunter was ''incredibly excited'' to receive Marsden Medal, which reflected the opinion of his scientific peers.
''It's a vindication of everything I've ever tried to do.''
He had always been collaborative, and the award also recognised the efforts of his fellow researchers, including many research students, he said.
Award officials said Prof Hunter had co-authored more than 140 publications, including papers in Nature and Science, and his research has been backed by many Marsden and FRST research grants.
Prof Hunter has already received Otago University's Distinguished Research Medal, and is a Fellow of the Royal Society of New Zealand.
Other Association of Scientists awards: Shorland Medal, to Prof Wei Gao, Auckland University, recognising his work, including on nano-materials and superconductors; the Research Medal, for researchers under 40, jointly to Prof Merryn Gott, Auckland University, and Associate Prof Richard Tilley, of Victoria University of Wellington; Science Communicators award, Dr Michelle Dickinson, Auckland University. firstname.lastname@example.org