The new organisations would have to be based outside of Auckland, Wellington and Christchurch.
The $25 million in funding was for a period of three years and would come out of next year's budget. Mr Joyce said he envisaged funding the launch of between one and three new institutes over the next four to five years, depending on demand.
"Regional Research Institutes would focus on scientific research relevant to a particular region, with a strong emphasis on the effective transfer of research into new
technologies, new firms, and new products and services," the minister said in a statement.
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As announced last month, today's budget also put another $80 million over four years into research and development grants distributed by Callaghan Innovation.
The grants, which last for up to three years, allow innovative New Zealand-based companies to recoup 20 per cent of any R&D spending, to a maximum of $17.5 million.
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Another $1 million has been allocated to attracting multinational companies overseas to undertake R&D in New Zealand.
And $3 million has been put aside for an annual reporting programme on New Zealand's science and innovation sector.