Science, technology, engineering and maths courses would have $690 million in funding cut under the Coalition's university reforms, Science and Technology Australia has warned.
It comes as a Senate Inquiry into the Job-Ready Graduates legislation heard the changes in funding would have damaging impacts on STEM education despite the government's effort to drive students into those degrees.
Chief executive Misha Schubert said the Job-Ready Graduates legislation as it is written would cut the overall funding per student by 17 per cent for maths degrees, 16 per cent for science and engineering degrees and 29 per cent cut in environmental science degrees.
"We really need more STEM graduates for the country in the next decade and beyond because we know that STEM skills are going to become increasingly important to the types of new jobs we hope to create in the economy," Ms Schubert said.
"And so those STEM faculty members have told us that this will make it very, very difficult to sustain staff numbers in the STEM faculties as they currently are because it would be making such big reductions in the level of income that's coming in through funds for education."
Ms Schubert said resource-intensive courses such as heavy engineering degrees and regional institutions with fewer students would feel the impact of funding cuts more acutely.
The peak body has urged the Senate to amend the draft legislation to protect the current resourcing level for STEM courses by adding a science loading clause to the legislation so overall funding for STEM education does not fall.
"We proposed the idea of adding a science loading to essentially top it back up to the current level of resourcing for the science and STEM disciplines so that you would remove the incentive in the currently drafted legislation for universities to offer fewer STEM course places and help better deliver on the government's stated intention," Ms Schubert said.
Australian Council of Deans of Science executive director Professor John Rice told the Senate inquiry the legislation would be detrimental to the quality of university teaching and research in the sciences and would not encourage more students to enrol.
"If you want more students to study STEM, then you have to invest a lot more in the teaching workforce in primary and high schools so that they've got the tools and the knowledge and resources to be able to bring the subjects to life for the students," Professor Rice said.
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When Education Minister Dan Tehan was asked how he could be sure there would be no cut to the quality or number of places in STEM degrees, he said the Job-ready Graduates package would grow the number of university places for domestic students by 100,000 in ten years.
"That means more Australian students will get a university degree. Under the package, students will pay 20 per cent less for a science degree," Mr Tehan said.
"University funding will grow by $2 billion to 2024 and we will establish a $900 million National Priorities and Industry Linkage Fund - with a strong focus on investment in STEM industries - to support universities to produce job-ready graduates for their local industries and communities."
Ms Schubert said the level of funding in the new industry linkage fund was not guaranteed by the legislation, meaning it could be changed by any future government or minister without the permission of the parliament.
The Senate committee for education and employment will deliver its report on September 25.