This created a "micro-managed environment", pushing the limits of meaningful performance indicators, and resulting in more elevated stress levels in scientists, she said.
"Conversely, a lack of appropriately sized science funding creates a work environment that places increased pressure on mental health, which is specifically part of what the wellbeing budget tries to address.
"We have to be careful when well-meaning initiatives indirectly contribute to what they try to fix."
Another leading New Zealand scientist and past president of the association, Associate Professor Nicola Gaston, said while $155m seemed like a big boost to tertiary tuition subsidies, at a 1.8 per cent increase, this would only slightly alleviate some of the pressures associated with inflation.
"As I calculated recently, a PhD student today would need to be paid a third more to match the PhD stipend I was paid in 2003, accounting for inflation; these pressures really do matter as they impact on wellbeing and productivity."
Gaston, the co-director of the MacDiarmid Institute for Advanced Materials and Nanotechnology, said her immediate question for the Budget was whether it would put numbers and action around this Government's commitment to act on climate change.
She acknowledged the $27m investment already announced for a National New Energy Development Centre in Taranaki, along with another $20m for research into low-emission technologies.
"It is really positive to see the Government invested in making it clear to Kiwis that there are solutions to some of the problems caused by climate change that we can solve here in New Zealand," Gaston said.
"Relatedly, though on a smaller scale, it is positive to see the initiatives being put in place around zero-waste, including product stewardship schemes for lithium batteries."
More fresh science funding – $25m over four years – would be targeted at helping solve New Zealand's agriculture emissions headache, with methane and other pollutants from farming making up around half of the country's greenhouse gas inventory.
Overall, the Budget allocated around $106m of operating funding over four years and $50.6m capital into innovation, with initiatives to support businesses to become more productive and develop high-value, low-emissions products.
A total $25.5m over four years specifically went toward growing start-ups.
"Having sustained support will mean that innovators can more effectively commercialise science and research and turn ideas into products and services which can then be successfully brought to market," Science and Innovation Minister Megan Woods said.
The Government had a target to invest 2 per cent of New Zealand's GDP into R&D by 2027.