Universities are pleading with the Abbott government to abandon its threat to axe funding for major programs supporting 30,000 researchers if the Senate refuses to support the deregulation of university fees.

Peak body Universities Australia warns in its budget submission that researchers on the verge of major breakthroughs in health, climate science and manufacturing will move overseas if funding for the Future Fellowships scheme and National Collaborative Research Infrastructure Strategy (NCRIS) expires.

Education Minister Christopher Pyne. Credit:Photo: Andrew Meares

Education Minister Christopher Pyne has repeatedly said that continued funding for both programs - which have been described as the "backbone of research in Australia" - is contingent on the government's higher education reforms passing the Senate.

"Given the profound significance of both programmes in underpinning Australia's research capability, Universities Australia strongly recommends that funding for both programmes be provided on an ongoing basis, irrespective of the outcome on the current higher education reforms," Universities Australia says in its submission.