The Russell Group, which represents the UK's top 20 universities, including Glasgow and Edinburgh, issued the stark warning to the Westminster government.
Universities south of the Border are facing major reductions in state funding, because of public service cuts announced by Business Secretary Lord Mandelson to cut the UK deficit.
Funding for Scottish universities in the last Scottish Parliamentary budget rose by 2 per cent, but fears remain that the English cuts could damage the nation's reputation, including Scotland's.
Russell Group leaders said: "It has taken more than 800 years to create one of the world's greatest education systems, and it looks like it will take just six months to bring it to its knees."
They added: "If government targets these huge cuts on university budgets they will have a devastating effect, not only on students and staff, but also on our international competitiveness, national economy and ability to recover from recession."
The group, which also includes Oxford and Cambridge universities, warned that 30 institutions could disappear and others face financial "meltdown".
The cuts to universities in England amount to a third of their annual spend. In last month's Pre-Budget Report, UK ministers announced they would slash 600 million by 2013. This is on top of 180m the government has asked universities to find in "efficiency savings" by 2011. A further 135m of cuts has been asked for by Lord Mandelson.
In Scotland, where responsibility for funding universities has been devolved, major cuts have not been announced.
There are fears Scottish institutions might fall behind their international competitors, including England, because of the access to extra funding from the introduction of tuition fees south of the Border.
A spokesman for Universities Scotland said the Scottish Government had managed to provide a 2 per cent real-terms increase in funding for institutions north of the Border.
However, it is feared the recession could also force cuts north of the Border.
A Scottish Government spokeswoman said: "Scottish universities' share of government spending has increased 3.87 per cent since May 2007. The draft Budget (from September 2009] sees a real-terms increase of 2.1 per cent in universities resource budgets. Universities have a cash increase of just over 35 million in resource funding since 2009-10."
The Russell Group represents the leading universities in research and teaching. It includes Birmingham, Bristol, Cambridge, Cardiff, Imperial College London, King's College London, Leeds, Liverpool, London School of Economics, Manchester, Newcastle, Nottingham, Oxford, Queen's University Belfast, Sheffield, Southampton, University College London and Warwick.