Downing Street has criticised "irresponsible" lecturers in London who praised protesters who stormed the building which houses Conservative HQ.
Windows were smashed and police officers were among those hurt when a minority of protesters turned violent.
Lecturers at Goldsmiths criticised unions for distancing themselves from the occupation of Millbank Tower.
They said the "real violence" was the cuts. However Goldsmiths "completely disassociates" itself from the remarks.
Meanwhile the Metropolitan Police have confirmed that 54 people have now been arrested over the demonstration, of which "the majority" described themselves as "students or a variation thereof". The oldest is in their early thirties and 10 were under 18.
A 23-year-old man suspected of throwing a fire extinguisher at police from the roof of the building has been arrested in Cambridgeshire.
The National Union of Students, which organised the march, has condemned the violence as "shameful, dangerous and counterproductive" and the UCU lecturers' union said it was the "actions of a mindless and totally unrepresentative minority".
But a statement from the president of the lecturers' union at Goldsmiths, part of the University of London, congratulated staff and students "on the magnificent anti-cuts demonstration" adding: "We also wish to condemn and distance ourselves from the divisive and, in our view, counterproductive statements issued by the UCU and NUS leadership concerning the occupation of the Conservative Party HQ.
"The real violence in this situation relates not to a smashed window but to the destructive impact of the cuts and privatisation that will follow if tuition fees are increased and if massive reductions in higher education funding are implemented."
Those remarks were criticised by Conservative peer Lord Tebbit, who said: "I can imagine what they would say were a group from the TaxPayers' Alliance to turn up at their homes and vandalise them in protest at the way these lecturers are leeching the taxpayer and failing to discipline their students."
And a Downing Street spokesman said: ''Praising violence over peaceful protest is frankly irresponsible.''
Authorities at Goldsmiths also distanced themselves from the comments.
"This statement in no way reflects the views of Goldsmiths, University of London. We completely disassociate ourselves from what has been reported.
"Our position echoes that of the University and College Union and of the National Union of Students in that it was deeply saddening to see a peaceful protest tarnished by utterly unacceptable behaviour."
The Conservative MP Greg Hands called on Labour deputy Harriet Harman to discipline some Labour MPs, after a Daily Mail article claimed they had "cheered on student vandals".
But the MPs in question rejected suggestions their comments on the micro-blogging site Twitter amounted to encouraging the violence.
Tom Blenkinsop, who quoted Nick Clegg as having warned of "riots" if extreme cuts were introduced, wrote: "Daily Mail say I was gleeful over the student riots. I wasn't. Am I surprised that Lab MPs are being attacked for defending the NUS? Not at all." He had also "tweeted": "Anyone involved in the violence should realise that by attacking police you are attacking allies in the public sector."
The Metropolitan Police has begun an inquiry into the handling of the student march. Those arrested - mostly for criminal damage and aggravated trespass - have been released on police bail until February.
The violence overshadowed the largely peaceful protests against the plan to lift the annual cap on university tuition fees in England from the current £3,290, to up to £9,000 a year for some institutions. They were also protesting against plans to cut higher education funding and teaching grants.
About 2,000 split from the main march to gather outside 30 Millbank, a building which includes the offices of the Conservative headquarters, where windows were smashed, fires lit and missiles thrown at police.
Metropolitan Police Commissioner Sir Paul Stephenson has said the police should have better prepared and called Wednesday's events "an embarrassment".
Policing minister Nick Herbert said police had "struck the wrong balance" when preparing for the protests.
About 225 officers had originally been deployed to police the march, the minister said, although a further 225 were called in as the situation developed.
Hundreds of coachloads of students and lecturers travelled to London from across England, Wales and Scotland for the demonstration in Whitehall.
Under the coalition's plans, students would not have to pay anything "up front" and as graduates, would only have to pay back their tuition fee loans once they were earning £21,000 or more.
But the NUS and other opponents say the prospect of such large debts will deter young people from poorer backgrounds from going to university.