Special Branch officers are being deployed in universities particularly at risk of being targeted by Islamic extremists, the BBC has been told.
Higher Education Minister David Lammy said the government was concerned about a number of institutions.
Speculation that alleged bomber Umar Farouk Abdulmutallab was radicalised at University College London has raised concerns about campus extremism.
But UCL's provost said universities cannot be a bulwark against terrorism.
Mr Lammy told BBC Radio 4's The Report, "We have identified universities for whom the risk is greater and they have to work closely with Special Branch, and so I think it is a partnership between leadership at universities and the police."
He added, "We do not recognise a caricature of a significant risk across Britain.
"But we do recognise that threat levels have been raised and that this is an extremely serious issue and that there are particular institutions - and those institutions are aware of this because we have brought it to their attention - where the risk is greater and those institutions are working very closely with the police and are working closely with Special Branch and those institutions [police and Special Branch] are present on campus."
Mr Lammy declined to name the institutions in question, saying he did not think that would be "helpful".
He also refused to be drawn on whether university Islamic societies should be monitored more closely.
"Universities are autonomous," he said. "They work closely with the police and the intelligence services, and I'm not going to comment further than that."
Terror link denied
The arrest of Mr Abdulmutallab, a former president of the Islamic Society at University College London (UCL), for allegedly trying to blow up a flight to Detroit on Christmas Day, meant he was the sixth member of a UK student Islamic Society to be arrested for suspected terrorism offences.
However, the body representing Islamic Societies in universities denied there was any link between student groups and terror plots.
Qasim Rafiq, of the Federation of Student Islamic Societies (Fosis) told the BBC: "There is no evidence or no substantial evidence to suggest there is a radicalisation of extremism taking place on campus, as people have suggested."
He said students were more likely to be radicalised by watching the "bombs fall on Iraq".
But Ed Husain, a former member of radical Islamist group Hizb-ut Tahrir, who now runs the Quilliam Foundation, a counter-extremism think tank, said he was concerned at the hard-line mindset in many campus Islamic societies.
He said: "In some university campuses on Friday prayers and most university campuses with their prayer rooms - and I have visited several of those - you see the literature that is stocked, the level of discussion that is happening, I am not saying it supports terrorism but it clearly does provide extremist mood music to which suicide bombers dance."
Prof Anthony Glees who wrote a 2005 report warning that campuses had become a safe haven for extremists said many universities were in denial.
One vice chancellor had told him to stop this research in the name of free speech but Prof Glees told the BBC academics should "challenge their students" about extremist views.
He added that universities should not be used as venues for extremist propaganda.
"Universities should be about rational debate and balance," he added.
Prof Malcolm Grant, Provost of UCL, said universities had a responsibility to work closely with security services but "not as policemen".
He added, "I would not ever want anybody to believe that we can be the bulwark against terrorism.
"I'm deeply concerned that there's an assumption that simply by installing simple measures of preventing, shall we say, radical speakers from coming onto campus, we're going to make a ha'p'orth of difference to this issue.
"Now let's be real about this. The influences on young minds are many and various."
The Report is on BBC Radio 4 on Thursday, 4 February at 2000 GMT. You can also listen via the BBC iPlayer after broadcast or download the podcast.