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The money, provided over two years, is from the the Encouraging and Supporting Innovation Fund of the Tertiary Education Commission.
The three universities are also working closely with three successful business entrepreneurs to build a collaborative culture, and to build technology-based enterprises resulting from university research.
Three entrepreneurs in residence, each linked to one university, have been appointed, comprising Dr Peter Fennessy (Otago University ), Dr Garth Carnaby (Lincoln University) and Dr Bill Swallow (Canterbury University).
An industry advisory board has also been established.
Senior representatives of the universities discussed prospects for collaboration with the board members at the Dunedin Club last night.
The new programme will encourage and support innovation involving the universities in respect of science and engineering, including biotechnology, agriculture, health science and information communications technology (ICT).
Otago University officials said the university was already committed to developing commercial applications of university research through the Centre for Innovation and the applied science degree programme.
The initiative aimed to foster a culture of innovation more broadly within the university, officials said.
Prof Brendan Gray, who holds the Dunedin City Council Chair in Entrepreneurship, said the approach was complementary, using the strengths of each university, including biological sciences at Otago.
Prof Don Roberton, the Otago University pro-vice-chancellor, health sciences, said that the new programme would help to develop potentially commercial applications of university research for the public good, including new drugs or medical equipment.
The programme would provide staff and students with insights into the potential and challenges of commercialising technology, officials said.
Advisory board members include Sue Suckling, chairwoman of the National Institute of Water and Atmospheric Research, NZQA and AgriQuality New Zealand Ltd; Jim McLean (chairman NZBio, HortResearch); Mike Dunbier (former chief executive Crop and Food Research); Richard Garland (MD NZ Pharmaceuticals) and David Band (ex PA Consulting and Sibson, UK).