Nick Herbert told MPs police would learn lessons after 41 officers were injured when a section of demonstrators stormed the Conservative party HQ.
The prime minister has also condemned the violence, which led to 50 arrests.
The Met Police has announced an inquiry into the handling of the march against a rise in university tuition fees.
Fifty people who were arrested during the protests over planned university fee increases have been released on police bail until February.
The majority had been held for criminal damage and aggravated trespass.
Thousands of students had taken to London's streets to join the demonstration against the plan to lift the cap on tuition fees to £9,000.
Around 2,000 split from the main march to gather outside 30 Millbank, the Conservative headquarters in Westminster, where windows were smashed, fires lit and missiles thrown at police, Mr Herbert said.
"It is now clear that a small hard core within this group were intent on violence," he told the Commons.
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.
"The police have to strike a balance between dealing promptly and robustly with violent and unlawful activity on the one hand, and allowing the right to protest on the other," Mr Herbert said.
"Clearly in this case the balance was wrong but these are difficult decisions and they are not taken lightly."
Earlier Mr Cameron called the protests "unacceptable" and said there had not been enough officers to control the crowds.
He called for the "full force of the law" to be used against those who had been violent.
Some protesters had broken into the Millbank building, although hundreds of workers, including Tory party staff, had already been evacuated.
And Mr Cameron said he was watching what had happened on television from Seoul, where he was attending a G20 summit.
"I was worried for the safety of people in the building because I know people who work in there, not just the Conservative Party, but other offices as well, and so I was on the telephone", he said.
He said protests were a part of democracy but violence and law-breaking was not.
Metropolitan Police Commissioner Sir Paul Stephenson has said the police should have better prepared and called Wednesday's events "an embarrassment".
He said: "It's not acceptable. It's an embarrassment for London and for us."
Police are continuing to examine CCTV footage of the incident.
The National Union of Students (NUS) said about 50,000 people joined the demonstration, but according to Scotland Yard, no trouble was anticipated.
Prime Minister David Cameron acknowledges there were too few police at the fees protests.
Labour deputy leader Harriet Harman said the party supported the inquiry and added: "We deplore the violence which marred an important demonstration which the tens of thousands of students who took part and their leaders had intended to be completely peaceful".
But shadow business secretary John Denham said the students had a legitimate cause and needed to be listened to.
He said: "Those parents and the students who were there yesterday have a legitimate cause that needs to be taken up and debated.
We mustn't allow the despicable action of some protesters to divert attention from a real issue."
Hundreds of coach loads of students and lecturers travelled to London from across England, Wales and Scotland for the demonstration in Whitehall.
As well as higher fees, they were protesting against plans to cut higher education funding by 40% and to all but wipe out teaching grants except for science and maths.
'Lost sympathy'
However Mr Cameron said he would not abandon his plan to reform tuition fees to allow some institutions to charge up to £9,000 a year.
NUS president Aaron Porter said he believed members had "lost a lot of public sympathy" because of what happened.
But Clare Solomon, president of the University of London Student Union, predicted a growing wave of similar protests in coming months.
London Mayor Boris Johnson said he also hoped those responsible for violence "paid a serious price for their actions".
Angry scenes at Milbank Tower at student fees protest
Asked about his decision to sign an NUS pledge promising to fight any rise in fees, Mr Clegg told ITV1's Daybreak: "I should have been more careful perhaps in signing that pledge.
At the time I thought I could do it."
But Shadow Commons leader Hilary Benn said Mr Clegg knew exactly what he was doing.
"Before the election [the Lib Dems] made everything of their pledge to vote against the lifting of tuition fees, after the election they couldn't dump it fast enough."
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.
