UNIONS claim plans for widespread mergers in the third-level sector will unfairly hit students and lecturers.
The Higher Education Authority (HEA) is finalising a report aimed at reducing the number of publicly funded colleges from 39 to 15.
It will involve mergers particularly in the institutes of technology (IT) sector, and greater collaboration generally between colleges.
The aim is to improve quality while also achieving greater efficiencies, such as getting the maximum use of college spaces at a time of increasing demand for higher education.
The Teachers Union of Ireland (TUI) represents about 4,000 lecturers in institutes of technology.
Deputy general secretary Annette Dolan said there was an unfair targeting of that IT sector, while universities escaped unscathed.
And the Irish Federation of University Lecturers (IFUT) asked about the impact on students who, as a consequence of mergers and some closures, would inevitably be forced to travel greater distances to study and pay for accommodation.
Closure of institutes of technology is not part of the plan, but the goal is for a smaller number of multi-campus "super ITs".
Each of these would be under a single administrative structure and would offer greater specialisation.
Wasteful duplication of courses is one of the issues that the rationalisation is intended to address.
In some cases, stand-alone ITs and some smaller colleges are being urged to align themselves to bigger colleges.
A number of institutes of technology are already involved in strategic alliances, with ambitions to be promoted to proposed Technological University status.
The proposed changes will have implications for the working conditions of college lecturers, who may, for instance be required to travel between campuses.
It is also intended that reform of the third-level sector will include issues such as the length of the academic year, although that would be addressed separately from this process.
The HEA published its proposals on Tuesday and will have final recommendations for Education Minister Ruairi Quinn by the end of March, after a process of consultation with the colleges in coming weeks.
Ms Dolan said that the publication of the HEA document was "extremely badly timed", coming as it does at the start of negotiations between unions and public service management on an extension the Cork Park Agreement.
She said: "It is an uncertain and confusing time for workers across the public service and this ill-timed act by the HEA will add more uncertainty and lead to further stress and concern for our members."
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