Visa restrictions are being considered that could limit foreign academics' access to the UK, a move described as potentially "disastrous" by Universities UK.
The Migration Advisory Committee (MAC), which provides independent advice to the Government, is consulting on possible changes to "Tier 1" and "Tier 2" of the new points-based immigration system.
Under the system, Tier 1 covers highly skilled workers who are not sponsored by their employers, while Tier 2 covers skilled workers who are.
If proposed changes are adopted, entry to Britain under Tier 2 would be limited to people working in a list of "shortage occupations" that suffer from a dearth of workers within the European Union.
Teaching and research are not considered shortage occupations - even when teaching is in a shortage subject.
The MAC is also seeking views on whether Tier 1 should be changed to reflect "changing economic circumstances" - in effect, protecting British jobs.
UUK has called for Tier 1 to remain unchanged and warned that the plans for Tier 2 would damage Britain's long-term competitiveness.
Both of the tiers in question already represent a restriction on previous arrangements: universities used to be able to recruit foreign staff on initial five-year work permits, but the points-based system offers initial visas for only three years.
At present, employers have to meet a "resident labour-market test" and show that they cannot fill a vacancy by advertising to home and EU citizens alone before they look further afield.
Under the MAC proposals, this test could be scrapped, with Tier 2 visas limited to workers in shortage occupations instead.
The proposals would result in the closure of academic programmes and the loss of international academics working in strategically important subject areas, UUK argued.
"Their contribution enables the UK to continue to support teaching and research in key areas where UK/European Economic Area nationals are in declining numbers," it said.
UUK said that the points-based system was already causing problems as it stands, adding that one department at the University of Cambridge, which it did not identify, would have lost a research grant worth more than £2 million if the restrictions on overseas academics instituted by the existing Tier 2 rules had been in place two years ago.
"Any further restrictions would result in the loss of further research funding," the body added.
As Times Higher Education reported last week, Dominic Scott, chief executive of the UK Council for International Student Affairs, has claimed that in the first few weeks of the new points-based system's operation, refusal rates soared to more than 60 per cent.
There is a fear that academics who are put off by tough immigration rules will simply join rival institutions abroad, weakening the UK's competitiveness.
UUK said that further changes to the rules on top of the upheaval that the sector had already faced could cause "confusion, create additional complexity and lead to even less consistent advice from the UK Border Agency".