Tens of thousands of students were joined by lecturers and parents during a national day of action against the controversial changes.
Organisers said the marches, occupations and sit-ins were an opportunity for protesters to make their voices heard peacefully.
But Westminster bore the brunt of lawlessness a fortnight after the Millbank riot as two police officers and 11 people were injured.
At least 15 protesters were arrested for offences including violent disorder, theft and criminal damage as barriers were thrown and fires lit in the street.
The clashes centred around a stranded police van that was ransacked and looted a short distance from the entrance to Downing Street.
Police were forced to "kettle" hundreds of protesters for around four hours a short distance from the Houses of Parliament as tensions ran high.
The tactic was widely criticised after around 5,000 people were penned in outside the Bank of England during the G20 protests last year.
Thousands also joined protest marches in Manchester, Liverpool and Brighton as pupils walked out of school in Winchester, Cambridge, Leeds and London.
Meanwhile students occupied buildings in Oxford, Birmingham, Cambridge, Bristol, Plymouth and in the capital.
Two protesters were arrested in Cambridge for obstruction, one in Liverpool for egg throwing and four in Manchester for public order offences and obstruction. Two people, a 15-year-old boy and 41-year-old man, were also arrested in Brighton.
In London, protesters had planned to demonstrate outside the Liberal Democrat headquarters, after leaders said they will break a pledge to abolish tuition fees.
Deputy Prime Minister Nick Clegg defended his uncomfortable new position during a visit to a south London school to mark the launch of the coalition's education White Paper.
He said: "What you will see is a system that will make access to university much much fairer than it is at the moment.
"It is simply outrageous, that more young people go from two private schools, Westminster and Eton, to Oxford and Cambridge, than thousands of youngsters who leave school every year.
"We want to change that. We want to make universities open and accessible to everyone, and that is why our reforms will mean that people who come from disadvantaged backgrounds will find it easier to go to university, cheaper to go to university."
Prime Minister David Cameron's spokesman said: "People obviously have a right to engage in lawful and peaceful protest, but there is no place for violence or intimidation."
The protests were dubbed Day X, with parents, teachers and trade unionists invited to join students at rallies organised by the Education Activist Network and campaign group Youth Fight For Jobs.
Senior officers deployed extra reserves in the capital today after police were caught off guard by an attack on the complex of buildings housing the Tory party headquarters on November 10.
The 50,000-strong demonstration resulted in 68 arrests so far and police continue to scour hours of video footage and thousands of photographs in a bid to identify those responsible for crimes.
Hampshire student Edward Woollard, 18, appeared in court today to admitted violent disorder after he was caught on camera dropping an empty fire extinguisher from a seventh floor rooftop.
Students were protesting against plans to increase tuition fees in England to £9,000 per year and to withdraw funding for university teaching budgets on many subjects.
The main protest march was stopped by lines of dozens of officers in Whitehall today before it could reach Parliament Square as around 10,000 people gathered in central London.
There were sporadic violent clashes as some demonstrators hurled missiles, climbed fencing and attempted to wrestle metal barriers from police as others set off fireworks.
The ugly scenes took place a stone's throw from 10 Downing Street and the Royal United Services Institute (RUSI) where Met boss Sir Paul Stephenson has been giving a speech on terrorism.
In other areas of Whitehall there was a party atmosphere, with students jumping up and down to dance music and holding a mass hokey cokey as helicopters hovered overhead.
The Metropolitan Police said a woman police officer suffered a broken hand and a male officer knocked unconscious on the fringe of the Whitehall people pen is being treated for leg injuries.
View the protest in pictures
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