Cash boosts for our largest funds for mission-led research have been welcomed by New Zealand's independent government body for the sciences.

Amid today's Budget announcements were allocations of $113.8 million over four years for the newly-refocused Endeavour Fund and $66 million over the next four years for the Marsden Fund.

The Endeavour Fund, previously known as the Ministry of Business Innovation and Employment Contestable Fund, has been re-focused towards longer-term, high impact, mission-led programmes of science.

The fund would invest in science that had a "strong potential impact" on New Zealand's economy, environment and society and would increase in size from $182.7 million in the 2015/16 year to $200.4 million by 2019/20.

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Meanwhile, the boost to the Marsden Fund - which remains the country's leading fund for "blue-skies" research - would see its annual amount increase by 49 per cent over four years, growing it from $53.6 million in 2015/16 to $79.8 million in 2019/20.

The two increases were among a $410.5 million package for science and innovation announced by the portfolio's minister, Steven Joyce.

Royal Society of New Zealand chief executive Dr Andrew Cleland said the society was "extremely pleased" to see the government increasing investment in scientific research and innovation and moving further towards the long-term goal of it contributing 0.8 per cent of GDP.

Dr Cleland also welcomed two other big investments among the package - $97 million over the next four years in health research, which was announced last week, and $15 million over four years of increased investment in the Catalyst international Fund, supporting more collaborative projects between Kiwi and international researchers.

"New Zealand needs to retain more of our excellent researchers and providing more opportunities for funding and international collaboration will contribute significantly to allowing us to do that."

Another area of research to benefit from Budget 2016 was agricultural greenhouse gas emissions, with the Global Research Alliance receiving $20 million over the next four years.

The funding would help the alliance progress its research through proof-of-concept work to pilot studies and commercialisation, while supporting international initiatives that addressed mitigation of emissions from livestock.

Antarctica New Zealand would meanwhile receive $16.7 million over four years, sustaining the Christchurch-based body's logistics and services to support science on the ice.

Other boosts went to the Maori Innovation Fund ($4 million over four years) the Accelerators Programme ($3 million over four years) and the Pre-Seed Accelerator Fund ($12 million over four years).

Mr Joyce said the new science funding - itself announced as part of the Government's wider "Innovative New Zealand" programme" - would see cross-government investment in science reach $1.6 billion annually by 2019/20.

"This very significant investment shows how committed this Government is to science-led innovation to strengthen and future-proof the New Zealand economy," Mr Joyce said.

"Innovative New Zealand is a major step towards delivering on the vision of the National Statement of Science Investment, and also supports the Business Growth Agenda, which seeks to grow business investment in R and D to over one per cent of GDP."

This very significant investment shows how committed this Government is to science-led innovation to strengthen and future-proof the New Zealand economy.

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Science commentator Professor Shaun Hendy, director of the University of Auckland-based centre of research excellence Te Punaha Matatini, said the Budget followed up on the direction signalled in last year's national statement.

"The focus of science and innovation spending over the last few years has been on growing business R and D, so it is pleasing to see a rebalancing towards science-led research," he said.

"We've seen a great deal of change in the science and innovation sector in the last few years so it is also a relief to see that well-established programmes like the Marsden Fund are being grown without being tinkered with."

"We know that this fund is effective but it is heavily oversubscribed; by increasing its size significantly over the next few years we can only hope that this lifts success rates up above 10 per cent and eases the pressures on researchers."

An increase in the Endeavour Fund was also important, he said, as it would compensate for what he described as a "torturously slow" roll-out of the National Science Challenges.

"Likewise an increase in core funding for Crown Research Institutes (CRIs) could dampen the impact from losses the CRIs might be facing now that MBIE's contestable fund has become much less targeted."

Dr Warren Parker, chair of Science New Zealand, which represents the seven CRIs, said: "The increased level of public funding is substantial, and Government has committed to strengthening the connection between the excellent science done in New Zealand and getting it into practical application.

"This is a two-way connection, and is vital to ensuring we are doing the science that meets current needs and that also challenges and opens up new opportunities for both the public and private sectors."

Science and innovation highlights:

• A total $410.5 million for science and innovation, taking the Government's annual science investment to $1.6 billion by 2020.

• $113.8 million over four years for the new, re-focused Endeavour Fund, previously known as the Ministry of Business Innovation and Employment Contestable Fund.

• $66 million over the next four years for the Marsden Fund, increasing the annual amount available for the Marsden Fund by 49 per cent over four years, growing it from $53.6 million in 2015/16 to $79.8 million in 2019/20.

• $63 million over four years for the new Strategic Science Investment Fund.

• $97 million over four years for additional health research through the Health Research Council