Deputy vice-chancellor, research and enterprise, Prof Richard Blaikie was awarded the Royal Society of New Zealand's Hector Medal.
Prof Jim McQuillan, a leading chemist also based at the university's Dunedin campus, received the society's T. K. Sidey Medal.
Prof Michael Baker, of Otago's Wellington campus, was awarded the prestigious Liley Medal from the Health Research Council.
The country's highest science honour, the Rutherford Medal, was awarded to social scientist Distinguished Professor Dame Anne Salmond, of Auckland University, for her eminent work, including on Maori social structures and interactions with the European world, award officials said. Prof Blaikie, an Otago physics graduate, was honoured for his pioneering contributions to the field of nano-optics, where he had demonstrated light could be manipulated at scales much smaller than its wavelength.
He then developed several new techniques for nano-scale optical printing, for etching, writing, or printing at the microscopic level. This approach can be used to fabricate tiny electrical circuits. Prof McQuillan said he had also been delighted to gain the T.K. Sidey Medal for electromagnetic radiation advances, for his research into two areas of vibrational spectroscopy. He conducted the first surface-enhanced Raman spectroscopy experiments at Southampton University in 1973.
The light-scattering technique was now one of the main methods used to assess the structure and composition of materials and had been used widely in various applications, ranging from drug development to the detection of art forgeries, society officials said.
Last year, he was the lead author in an already highly-cited paper in the world's leading general medical journal, The Lancet. The paper presented a national study of five million overnight hospital admissions, showing a dramatic rise in the incidence of serious infectious diseases and rising inequalities across populations in New Zealand. The authors showed that Maori and Pacific people and the socioeconomically disadvantaged bore a disproportionate share of the burden, award officials said.
Also honoured were: Pickering Medal, Emeritus Prof Sir Harold Marshall, Thomson Medal, Dr Peter Lee, Callaghan Medal, Dr Siouxsie Wiles, MacDiarmid Medal, Prof Neil Broom, all Auckland University; Hutton Medal, Prof Dave Kelly, Canterbury University; Mason Durie Medal, Prof John Pratt, Victoria University of Wellington; R.J. Scott Medal, Prof Andrew Buchanan, Canterbury University.