In his first speech as Chancellor of the University of Oxford, Mr Patten said that the violent tactics of some anti-vivisectionists were undermining fundamental principles of liberal democracy.

The right of university researchers to pursue open and independent inquiry without fear of intimidation was one of the bastions of free society, he said.

This was now at risk from the campaign of harassment that has blocked a primate laboratory at the University of Cambridge and interrupted work on a similar facility at Oxford.

Mr Patten was speaking as it emerged that new measures to clamp down on animal rights extremists are to be a centrepiece of the Queen’s Speech on Tuesday.

Ministers plan to outlaw protests in front of private homes and are also considering a new offence of “economic sabotage”.

Violent protests have prompted pharmaceutical companies such as Novartis to reconsider their presence in Britain, and threaten vital research into diseases such as Parkinson’s and malaria.

The dangers of capitulating to the extremists, however, stretch much more widely than this, Mr Patten said in the Save British Science lecture at University College, London. To do so would encourage other extremists to use harassment to discourage universities from studying particular branches of science and history, or from employing staff of certain ethnic or religious backgrounds.

“It would, of course, be devastating news for many who suffer from disease if this research was to be halted in its tracks,” he said. “But there is more at risk than the future of biomedical research in one university, or even in the whole country.

“To use violence against research at a university — against academic staff and all those in any way associated with what they do — is a serious blow against the basic liberties of a plural society. If we surrender over animal research, what comes next?

“Will there be attempts to intimidate us not to employ those who belong to a particular country or faith or ethnic group? Will research into some parts of our history be censored as it has been and still is in some countries?

“Will other sorts of scientific inquiry be choked off because of the objections of this or that group which is prepared to threaten or use violence? Pushing back the boundaries of knowledge is one of the hallmarks of a free and civilised society.”

The threat to Oxford’s animal laboratory was a threat to fundamental liberal values, said Mr Patten, whose term as a European Commissioner ended yesterday. “These are all issues that are on the frontier between an Enlightenment world of liberty and reason, and darkness.

“Universities, when able to pursue knowledge simply out of curiosity, are a bastion of a free society, as newspapers are. If you start to limit through the use of violent means what universities do, you are undermining the values of freedom.”

As well as a ban on demonstrations outside private residences, which will be announced in the Queen’s Speech next week, the Government is considering legislation to create a new offence of deliberately inflicting economic damage on companies engaged in legitimate business.

The proposed economic sabotage offence, however, has raised concern among civil liberties groups, who fear it could criminalise legitimate protest such as the boycott campaign against apartheid South Africa.

Oxford was last week granted an injunction banning protesters from a 50-yard exclusion zone around the half-built primate centre, and from a 100-yard area around around the homes of all university staff, students and alumni, contractors, subcontractors, suppliers and shareholders.

The ruling also prevents activists from harassing anyone with links to the facility verbally, by fax or by email, and from taking their photographs.

Mr Patten said the university was determined to complete the laboratory, and defended the terms of the injunction. “We intend at Oxford to complete the building. The injunction was sought in order to allow us to do that,” he said.

“There is no argument so far as people’s right to demonstrate peacefully is concerned, but that’s not what we have seen at Oxford, or what we have seen elsewhere in this country,” he added.

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