At the weekend former Australian coal industry executive Ian Dunlop wrote in the Fairfax newspapers that “science has disappeared from the government’s priorities, just at the time we need it most”.

Last week, Liberal backbencher Dennis Jensen went further, labeling the government’s science funding cuts “incoherent”.

“Unfortunately, I see no evidence to suggest an improvement in science policy,” he told the ABC. “In fact, the reverse would appear to be the case.”

It’s no secret that Joe Hockey’s first budget took the knife to many federal spending programs. But science and innovation were among the hardest hit areas. In addition to cuts to the CSIRO, there were cuts to basic research at the Australian Research Council, as well as cuts to the Australian Institute for Marine Science and the Australian Nuclear Science and Technology Organisation. Also slashed was funding for postgraduate researchers, for environmental science, clean technologies, water science and Cooperative Research Centres. There have also been huge cuts to R&D and innovation programs, and to virtually every federal renewable energy program.

Some of the budget cuts were hidden deep inside the budget papers. For instance, the government announced welcome new support for the CSIRO to operate its brand new research ship, the RV Investigator (Labor had built the ship, but neglected to fund any money to run it). But in Budget Paper 2, you can discover that part of the RV Investigator’s running costs must be provided by the CSIRO itself. At a time when the overall CSIRO budget is shrinking, the agency will have to find an extra $21m from within its existing resources to run the vessel. In effect, it is a funding cut.

Funding for Antarctic research carries a similar surprise. While the government will direct $24m towards the Antarctic Gateway program, as the budget papers explain, “the cost of this measure will be met through reprioritisation of the Australian Research Council’s existing funding”. The ARC’s funding is also declining, so this too is effectively a budget cut.

The funding cuts can only mean one thing: fewer jobs. According to figures compiled by Labor’s Kim Carr, the shadow minister for research and higher education, job losses in science as a result of the budget cuts will total nearly 1,000 full-time staff. These figures are not disputed by the industry minister, Ian Macfarlane.

The cuts to the CSIRO have grabbed the most attention, including internationally. With $111m slashed over coming years, the agency is set to shed nearly 500 jobs. Respected international scientific journal Nature blogged recently about the CSIRO’s woes. Leigh Dayton, at the prestigious Science magazine website, told readers that “the bad news just keeps coming for Australia’s scientific community.”

The inevitable outcome is big reductions in the CSIRO’s research output. According to the CSIRO’s recently released Annual Directions Statement, CSIRO will completely cease research in a number of fields, and shut down at least eight laboratories. Research fields slated to go include neuroscience, colorectal research, urban water research and marine biodiversity. Research will be scaled back in radio astronomy, astrophysics, renewable energy, metallurgy, Nano science, and social and economic sciences. Labs and facilities that will close include the Mopra telescope, the Aspendale laboratories, the Highett laboratory, the Ardig field station and the Griffith laboratory in the Riverina.

According to the president of the CSIRO’s staff association, Dr Michael Borgas, “There's a lot of concern and nervousness [about the cuts].” Borgas describes an organisation buffeted by constant crisis, emerging from round after round of internal restructures, followed by the latest budget cuts.

“In some areas where things are being closed down completely, there is an effort to hold on to remnants of the core capability so you could restart things in the future,” he told Guardian Australia. “It’s very hard to sustain and renew large tranches of the research agenda with these cuts going on.”

Inevitably, some of those laid off will leave scientific research altogether.

“People will be lost to science, no doubt about that,” Borgas said. “It’s a pity to waste all that investment, not just from the individual’s point of view, but investment that the nation has made over many decades.”

For the weary insiders used to the boom-and-bust cycle of research and development in Australia, it’s hardly a surprise. Australian science policy has long been trapped in short-term cycles of funding boosts and cuts.

“This has been the case for a while,” Curtin University radio astronomer Steven Tingay told Guardian Australia. “Over the last decade in Australia there have been many calls for a longer-term strategy for science that is not made up as we go along.” Tingay points out that international collaborations, like the Square Kilometre Array radio telescope, progress over decades and need long-term commitments from governments to proceed.

“Capacity has been built up and then scaled back, so it makes it very difficult to plan on the timescale of any sort of credible, high-impact research program,” he said.

Those at the coalface are increasingly concerned that the Abbott government is directionless when it comes to science and research.

In a post-budget interview, Australia’s chief scientist, Ian Chubb, bluntly argued that the current government has “no strategy” when it comes to science policy.

“I can see one emerging, but we haven’t got one,” he said.

Chubb argues that a coherent national strategy for science is essential. “We need a much more strategic approach to all of this, because I don’t think, in the highly competitive world that we live in, that all you can do is say, ‘We’ll do this, or a bit of that,’” Chubb said, pointing out that innovation is linked by long chains of interconnected research. “Nothing is not linked to something else, basically. These things do not exist in isolation.”

Nobel laureate Brian Schmidt told Guardian Australia that “by most measures Australia is already underinvesting in R&D.”

International data backs this up. According to recent OECD statistics, Australia ranks around the middle of the pack when it comes to various measures of research and innovation, such as the number of PhDs in the workforce, or government investment in research and development.

“I think the problem that we have right now is that every time we get a new program, the ground shifts,” Schmidt added. “I’m trying to plan my research program, like everyone else, five to 10 years out, and when we spend money and then switch it a few years later, we end up not getting very good value for the government’s investment.”

As a result, Australia ranks well below many of our trading partners and economic competitors when it comes to investment in scientific research. According to Chubb, “Australia is not good at innovating for export.”

Chubb cites data that shows only about 4% of Australian companies take new products to international markets. “You could probably argue that that figure’s too small,” he said. He argues programs to link basic research to business enterprise are crucial.

“If we’re going turn our economy into a very adaptable economy through innovation and getting the best value out of our researchers, then you’ve got to build a bridge.”

Most economists think that scientific innovation eventually drives economic growth, although predicting exactly how and in what form can be fiendishly tricky.

“There are widespread and important economic, social and environmental benefits generated by Australia’s … public funding support of science and innovation,” the Productivity Commission concluded in a report completed during the Howard government, in 2007. “On the basis of multiple strands of evidence, the benefits of public spending are likely to exceed the costs.”

Terry Cutler, a former CSIRO board member, was commissioned by the Rudd government to review Australia’s performance in research and innovation. He thinks the cuts to science, technology and innovation are “appalling”.

“I’m very concerned about the health of the CSIRO at the moment,” Cutler told Guardian Australia, “because you’ve got three things coming together which are going to put enormous stress on the organisations.”

“First of all you’ve had an incredibly significant internal reorganisation under way, starting earlier this year. At the same time you’ve had an outgoing CEO, so you’ve got that leadership uncertainty, and then you’ve got the additional budget pressures on top of the organisational changes.”

Cutler thinks it all adds up to “the potential … to seriously undermine the CSIRO’s ongoing viability.” He points out that the attacks on science in this budget are in contrast to the generally good record of the Howard government in supporting science and innovation.

“There's a remarkable lack of rationale – that to me to me is the most disturbing aspect,” Cutler said.

But in the austere reality of 2014, such comparisons hold little sway for the Abbott government. Apart from the cuts to basic science, the budget saw massive changes to the funding arrangements for universities, where the bulk of Australia’s basic research is carried out.

The chorus of anxiety from vice-chancellors is already growing. But the implications for Australian science could be just as serious.

Ian Chubb warns that “with the deregulating of university fees, for example, we don’t know what will happen with some courses.”

Chubb nominates the physical and mathematical sciences as courses potentially at risk under the new higher education paradigm.

“Will universities continue to offer courses which are expensive but which are not popular, which are very important to have somewhere in the country?” he said. “We do need a more systematic approach to make sure that we have talent and skills security, and put that alongside food and water security.”

For its part, the government argues that it continues to invest in science, including in critical areas such as the Future Fellowships program for top emerging researchers, and its new fund for medical research.

In an email, Minister Macfarlane told Guardian Australia that “this government is committed to science and will continue to support world-leading research and the role of science in our community.” Macfarlane pointed to $161m in new spending in the budget, such as new money to operate the CSIRO’s research vessel, $30m for the OPAL nuclear research reactor at Lucas Heights, funding for National Science Week, “over $25m to safely dispose of radioactive waste” and $10m to extend the Australia-China Science and Research Fund.

While acknowledging the CSIRO cuts, Macfarlane argues the government is still supporting it to the tune of nearly three-quarters of a billion dollars annually. “The CSIRO will receive over $3bn in government funding over the next four years,” he wrote.

None of this will appease the government’s critics. Labor’s Kim Carr told Guardian Australia that "this is a government that has no science minister, no science policy, no technology policy, and no jobs policy.”

“It's not interested in developing our capacity to attract new investment, so it's not just the thousand scientists that will lose their jobs, it is the knock-­on effects that taking out that type of capacity has on the broad economy and particularly industry,” he said.

The Greens’ Adam Bandt was even blunter. “Tony Abbott is the most anti-science prime minister we’ve ever had,” he said. “This is an ideologically motivated attack on scientific research.”

Meanwhile, at the CSIRO the redundancies are just getting started. The organisation recently laid off its world-beating legal team, responsible for winning more than $400m in royalties from giant tech companies using the CSIRO’s Wi-Fi patents.

For the CSIRO staff association’s Michael Borgas, it’s time to question whether the government is attacking the integrity of Australian science. “The real concern is what the long-term agenda of the government is,” he warned.