The Taoiseach, Ms Ahern, has distanced himself from plans by the Tánaiste, Ms Harney, which could give her Department a greater role in the allocation of the €2 billion-plus research budget.
Ms Harney's recent move to establish a National Commission for Research and Innovation has been seen as an attempt by the Department of Enterprise, Trade and Employment to gain greater control of research funding - at the expense of the Higher Education Authority (HEA) and the Department of Education.
In a policy document prepared for Fianna Fáil, Mr Ahern backs the current system in which funds are channelled to the universities via the HEA under the Programme for Research in Third-Level Institutions (PRTLI). The document points to the danger of returning to a situation where universities do not enjoy the freedom to establish their own research priorities.
The Fianna Fáil policy document makes no reference to the research commission established recently by Ms Harney. Instead, it says the Irish Research Council will continue to have an important role in advising the Government on research policy. The Fianna Fáil document states:
"We believe that there is a need to avoid any return to the days of an overly directed research programme and that it is key to allow a dynamic research community to evolve in line with the core principle of supporting excellence where it arises. As such, we will continue to support research on the basis of recognising the distinct, but also inter-connected role of different programmes, from individual grants up to more targeted support for areas of national strategic interest."
This is seen as a defence of the current situation, in which the HEA and the universities enjoy considerable freedom to decide research priorities.
The document points out there was no dedicated research funding available through the Department of Education in 1997. It states: "Since 1997, Fianna Fáil in Government have given clear and unprecedented support to third-level research."
It adds: "Under the PRTLI we are enabling third-level institutions to conduct world-class research by awarding funding to those institutions which have come through a rigorous competitive process."
The Fianna Fáil document is called "Keeping Ireland at the Cutting Edge: Science, Research and the Information Society".