University leaders have agreed to inform the police of any extremist behaviour by students or visiting speakers that they suspect may lead to terrorism.

A new “tool kit” for universities issued today by Bill Rammell, the Universities Minister, advises universities to draw up a national watch list of guest speakers who should be banned from speaking on campus. It also suggests that universities consider setting up multi-faith chaplaincies instead of separate prayer rooms for different faiths, to promote integration and prevent pockets of extremists forming.

Where they are allowed, Muslim chaplains should be trained to support vulnerable students who are being groomed, bullied or harassed by violent extremists so that these concerns can be passed to the police.

Mr Rammell was adamant, however, that Muslim students – particularly those coming from overseas – did not have the right to demand special treatment from British universities. “Britain technically is a Christian country with many secular features. It’s those two things. It’s not anything else. If you expect that you would have the same response to your faith needs in Britain as would happen within a Muslim or Islamic country, [you] would be disappointed,” he said.

Mr Rammell said that the biggest threat faced by Britain came from al-Qaeda-influenced terrorism. “Our judgment is that the threat in higher education is serious but not widespread,” he said.

He added that the Government had gained a greater insight into the terrorists’ minds since the last guidance on the subject was published in 2006.

“It reflects our increased knowledge of how violent extremist groups operate, how they recruit and what the scale and nature of this activity is within our communities,” he said.

Universities, which initially rejected the previous guidance as a threat to freedom of speech, accepted the latest version. Diana Warwick, the chief executive of Universities UK, representing vice-chancellors, said: “Violence, or the incitement to violence, has no place on a university campus.”

The Federation of Student Islamic Societies, which also criticised the previous guidelines, welcomed the revised document, although it insisted that there was still no evidence of an Islamic threat on British campuses.

The new guidelines have overcome previous objections by removing many references to extremism in the name of Islam and focusing on the importance of academic freedom.

Mr Rammell said that while it was legitimate and permissible to research the origins of violent extremism, and even to develop an understanding of what drives people to acts of terror, it was important not to move from this to advocacy of violent extremism.

His comments follow fears that some Islamic societies and prayer rooms in universities had become no-go areas for the authorities, where extremists may be free to preach hatred and violence to vulnerable students.

The guidance advises universities to make proper checks on student groups or outside bodies that book university premises for speaking events. Leaflets distributed on campus should be translated into English and students and lecturers should be advised to report suspicious activity, such as unusual internet use.

The Government hopes that the guidelines will help to prevent young Muslims from becoming radicalised. The guidance states that there is no single profile of potential recruits but they are likely to be younger than 30 and male, although the number of women who support and participate in violent extremism is increasing.

This comment followed the conviction of the “lyrical terrorist”, Samina Malik, a Heathrow airport worker who received a suspended jail term last year for possessing literature that could be useful to terrorists.

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