Students protesting against federal budget cuts to higher education have clashed with police as thousands of protesters marched through CBDs across the country.

The rallies were part of a national day of action against the Government's plan to deregulate university fees, and were organised by the National Union of Students (NUS).

Almost 2,000 people marched from Melbourne's State Library to Parliament House on Spring Street chanting, "No ifs, no buts, no education cuts".

As crowds were leaving Parliament, a group of about 20 students took over the intersection of Bourke and Spring streets.

Sorry, this video has expired Arrests after small group refuse to leave protest area

Protesters scuffled with police as they dragged the group off the road and one girl was pushed to the ground.

At least 13 people were arrested; they are expected to be charged on summons with blocking a roadway.

In Sydney, about 2,000 demonstrators sat in the middle of George Street and burnt a copy of the federal budget in a symbolic gesture against the uncapping of tertiary fees.

A 23-year-old man was arrested after a flare was let off as the group made their way from the University of Technology Sydney down George Street.

Another demonstrator was arrested and charged with assaulting police after a scuffle broke out when students tried to block traffic.

Both men will appear in court next month.

After gathering at Town Hall a group then attempted to blockade the road, but riot police moved in and forcibly stopped them.

At the Australian National University in Canberra, hundreds of students students tried to storm the administration building and small scuffles broke out between security and protesters.

Several hundred university students stopped traffic in Brisbane with a march and police intervened when a small, separate protest group surrounded and heckled Greens Senator Larissa Waters as she addressed the crowd.

Similar protests have been held around the country, with students also taking to the streets in Perth, Adelaide and Hobart.

Students say the protests are to express their anger over the Government's moves to overhaul the higher education sector.

The federal budget unveiled plans to deregulate university fees from 2016, allowing universities to charge what they like for courses.

The interest rate on student loans will also increase, and the income threshold for when students need to start paying the money back will be lowered.

The NUS says it wants proper public investment in universities rather than the buck being passed on to students.

NUS president Deanna Taylor says no-one can predict how high fees will go.

"But what we do know is that we are looking at six-digit fees, degrees in the order of hundreds of thousands of dollars, even for something like a teaching degree or a nursing degree," she said.

Abbott, Pyne cancel Deakin University visit over security concerns

The protests came after Prime Minister Tony Abbott and Education Minister Christopher Pyne cancelled a planned visit to Geelong's Deakin University, citing security advice from the Australian Federal Police (AFP), because of planned student protests.

However, Mr Pyne attended a fundraiser lunch for Liberal MP Sarah Henderson in Geelong this afternoon. Mr Pyne says the AFP advised him that the party fundraiser event was safe, but the university was not.

On Monday, former Liberal MP Sophie Mirabella had to be escorted by police out of a lecture at Melbourne University after it was disrupted by protesters.

It followed a similar incident at Sydney University last Friday when Foreign Minister Julie Bishop was mobbed by students who were angry about planned changes to higher education.

This morning Mr Abbott said he did not want to monopolise police resources and inconvenience others by going ahead with the trip.

Sorry, this video has expired Sydney students march in protest against budget

"Giving the students an excuse for a riot is not actually going to serve that purpose, it was going to take probably up to 50 police off the streets who may have been more useful elsewhere, it was going to inconvenience a lot of people," he said.

Federal Opposition Leader Bill Shorten says student protesters risk undermining their cause if they resort to violence and aggression.

"I say to these student radicals, 'Don't let Tony Abbott's crazy cuts and broken promises and lies before the election off the hook by making yourselves the issue'. Let people come and express their views in a peaceful manner," he said.

Foreign Affairs Minister Julie Bishop urged students to learn form her experience and protest peacefully.

"We just ask for the student protesters ... apparently it is a group called the Socialist Alternative ... we do ask for them to not intimidate people. Not confront people," Ms Bishop said.

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"They can protest of course - this is a free country - but do it peacefully and in a way that does not prevent events going ahead ... does not harm other people."

But NUS president Deanna Taylor says students are being made to look like violent rebel rousers.

"It's absolutely not the case. We want peaceful demonstrations. We want to be able to show our opposition in a peaceful way, and I suspect that there's more to the story than has been told so far," she said.

At the University of Technology Sydney (UTS), staff joined students gathering to protest against the uncapping of fees.

Vince Pauley from the National Tertiary Education Union says taking the cap off tertiary education will turn universities into businesses.

"That's great if you want to run a university as a money-making enterprise, but obviously universities should be about more than that," he said.

"They should be more than about dollars and cents. It's about people, it's about research, it's about educating people to be able to do that."

UTS staff are also striking against work conditions and the university's management and have set up a picket line to stop students reaching classes.