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Core science and innovation funding will drop by $10 million to $773.7 million in the next financial year, while business research and development and commercialisation will get a $24 million boost in reprioritised funding.
A further $12m of reallocated funding will go towards earthquake research to help rebuild Christchurch in the wake of February's destructive quake.
Science and Innovation Minister Wayne Mapp said today the Government was fully committed to science and innovation investment to help diversify the economy.
"Science and innovation are cornerstones in lifting New Zealand's economic growth. They also have a crucial role in dealing with natural hazards like earthquakes," Dr Mapp said.
The newly funded earthquake research would look at questions needing urgent answers, such as why stairs in some buildings collapsed, as well as long-term issues, such as better understanding the quake risks in Canterbury.
MacDiarmid Institute deputy director Shaun Hendy said while science and research spending had not been cut severely, New Zealand had for decades under-invested in research.
"These days developed countries need to invest heavily in science and technology just to stand still, so if New Zealand is to halt its plummet through the OECD (Organisation for Economic Co-operation and Development) rankings it needs more than just static government investment in this sector," Prof Hendy said.
The cut in research infrastructure spending was also disappointing, he said.
Science New Zealand chief executive Anthony Scott welcomed the provision of a guaranteed sum for each Crown Research Institute (CRI), which for the first time would guarantee a total $215m in core funding to the eight CRIs -- almost a third of total CRI revenue in the last financial year.
"While not new money, it is a significant step which will maximise the value that New Zealand gets from its science investment," he said.
"Having a reasonable sum of money enables a CRI to plan research programmes with confidence alongside its key stakeholders."
Otago University genetics researcher Peter Dearden said it was hard to envisage major funding increases in such difficult times, adding that it was important to invest to maintain and extend innovation.
But while science was not too badly affected overall, Dr Dearden said he was concerned about cuts to genomics, which he said was a blow to biological research in New Zealand.