An intensive lobbying campaign is under way amid concerns in third-level colleges that control of the €2 billion-plus research budget could pass to the Department of Enterprise, Trade and Employment.
The "turf war" between the universities and the Department follows the recent Government decision to establish a commission to examine the future of research spending.
There are fears in academic circles that the new National Commission for Research and Innovation could lessen the role of the Higher Education Authority (HEA) and the Department of Education in research funding and give an expanded role to the Department of Enterprise.
There is also the traditional clash between the academic focus on research per se and the Enterprise-led focus on research as a means of generating employment.
Senior academics have been lobbying Government officials about the potential dangers of any move which could undermine the current role of the HEA and the Department of Education in research funding.
The commission, which is being chaired by the former president of UL, Dr Edward Walsh, is said to have an "open mind" on a new framework for government policy on research and technological development.
One source said: "The commission will examine best international practice in the research funding area. The intention is to ensure that the best synergies are in place."
Concern among university heads was triggered by the decision of the Tánaiste, Ms Harney, to bring the commission proposal to Cabinet recently. It appears other relevant Government departments were given no notice of the plan.
The commission, which is expected to attract some leading international figures, will make recommendations on new structures and mechanisms for the implementation of research policy. The commission's brief will range across all aspects of research spending.
At present, research funding is mainly administered by the Department of Enterprise and the HEA. The HEA runs the Programme for Research in Third-Level Institutions (PRTLI).