An estimated 40,000 students from towns and cities across the UK have travelled to the capital for the rally which was organised by the National Union of Students (NUS) and University and College Union (UCU).
Speaking from the scene, Sky News’ senior correspondent Michelle Clifford said the police were not present in large numbers when the violence broke out among some of the students.
"It’s actually turned pretty violent, a few hundred protestors stormed into Millbank Tower.
"It was all peaceful – they were just shouting but now there are hundreds outside, smashing the windows, big eight foot windows of the tower have been smashed, there’s glass flying everywhere," she said.
Michelle added that the number of students vastly outweighs that of police officers.
The protesters want to persuade the Government to back down on plans to allow universities to charge tuition fees of up to £9,000 a year from 2012.
Banner-waving students marched and chanted alongside lecturers to show their anger at the planned 300% increase.
The Government last week confirmed students would have to pay back fees after graduation, with student finance repayment thresholds rising from the current £15,000 a year to £21,000 per annum.
The plans dominated Prime Minister’s Questions where Deputy PM Nick Clegg came under fire for his party’s U-turn after campaigning against a fees rise in the General Election.
Mr Clegg acknowledged that graduates who go on to high-earning careers will pay "over the odds" for their degrees as part of the shake-up of higher education funding.
But he insisted the Government’s plans were a "fair and progressive solution to a very difficult problem".
Labour’s deputy leader Harriet Harman said Mr Clegg had been "led astray" by the Conservatives during the negotiations to form the coalition Government.
Speaking before the march NUS president Aaron Porter said the proposals are "utterly unacceptable" and an "outrage".
He warned the Liberal Democrats that they will lose the support of a generation of young people if they continued to back the fee hike.
"We are taking to the streets in unprecedented numbers to tell politicians that enough is enough," he said.
"We will not tolerate the previous generation passing on its debts to the next, nor will we pick up the bill to access a college and university education that was funded for them.
"This Government is abdicating its responsibility to fund the education and skills provision we desperately need just as every other country is investing in its future.
"We cannot and will not accept that miserable vision for our future.
"We will fight back against attempts to dismantle the funded education system we desperately need for economic recovery, social mobility and cultural enrichment.
"The Government’s short-sighted and self-defeating cuts to colleges and universities must be resisted and that resistance begins now."
The Government says the increase in fees will make the system fairer, because students will not have to pay back their loans until they are earning more.
It also says it will be making more money available for scholarships for students from poorer backgrounds and there will be higher grants for students from families earning less than £25,000.
Money gained through the proposals will go towards plugging the gap left by swingeing cuts to the higher education teaching budget, announced in last
month’s spending review.
Tuition fees currently stand at £3,290 a year.
The march was also held in protest at planned cuts to the education maintenance allowance (EMA) which provides college students from the poorest backgrounds with extra financial support.