A Eurosceptic Tory MP has been accused of compiling a "hit list" of university professors who teach Brexit courses.
Downing Street has distanced itself from government whip Chris Heaton-Harris, who wrote to universities asking for the names of professors.
Lecturers reacted with fury to the letter, calling it a "sinister" attempt to censor them and accusing him of conducting a "McCarthyite" witch hunt.
Mr Heaton-Harris said he believed in "open" debate on Brexit.
The government whip tweeted: "To be absolutely clear, I believe in free speech in our universities and in having an open and vigorous debate on Brexit."
Mr Heaton-Harris is a member of the pro-Brexit European Research Group of Conservative MPs.
Labour accused the MP of seeking to draw up "what looks like a register of Brexit heretics" and branded the government response to it a "shambles".
The Liberal Democrats said the letter was "chilling" and that Mr Heaton-Harris should stand down from the government, adding that ministers should reassure universities that they were not expected to comply with his demands.
Downing Street said Mr Heaton-Harris had written to universities in his capacity as an MP and not as a representative of government.
The prime minister's official spokesman said Theresa May respected the freedom and independence of universities and the role they played in providing open and stimulating debate.
Commons leader Andrea Leadsom insisted Mr Heaton-Harris had not sent a "threatening letter" to universities, although she could not say why he had sought the information.
She told BBC Radio 4's The World at One: "It does seem to me to be a bit odd that universities should react in such a negative way to a fairly courteous request."
Sally Hunt, chairwoman of lecturers' union the University and College Union, said: "Our society will suffer if politicians seek to police what universities can and cannot teach.
"This attempt by Chris Heaton-Harris to compile a hit list of professors has the acrid whiff of McCarthyism about it and (universities minister) Jo Johnson must disown it in the strongest terms."
University lecturers took to twitter to mock Mr Heaton-Harris and the government over the letter.
Like other academics on Twitter, I declare forcefully that I will not reply to a letter which wasn't addressed to me. That'll show him.— James Chalmers (@ProfChalmers) October 24, 2017
Professor David Green, vice-chancellor at the University of Worcester, said: "When I read this extraordinary letter on Parliamentary paper from a serving MP, I felt a chill down my spine. Was this the beginnings of a very British McCarthyism?"
He said he feared he would be denounced in Parliament by Mr Heaton-Harris as an "enemy of the people" if he did not supply the list - something he said he had no intention of doing.
He added: "I realised that his letter just asking for information appears so innocent but is really so, so dangerous.
"Here is the first step to the thought police, the political censor and Newspeak, naturally justified as 'the will of the British people'."
The Guardian revealed that Mr Heaton-Harris wrote to university vice-chancellors at the start of this month asking for the names of professors "involved in the teaching of European affairs, with particular reference to Brexit".
The MP's letter also asks for a "copy of the syllabus" and online links to lectures on Brexit.
Lord Patten, the chancellor of Oxford University, and former chairman of the BBC Trust, described Mr Heaton-Harris's letter as an "extraordinary example of outrageous and foolish behaviour - offensive and idiotic Leninism".
The peer, a longstanding supporter of Britain's membership of the EU, told BBC Radio 4's The World At One: "I couldn't believe that it had come from a Conservative MP.
"I think he must be an agent of Mr Corbyn intent on further increasing the number of young people who want to vote Labour."
He said he was sure most university vice-chancellors would drop the letter "in the waste-paper basket" and he accused Mr Heaton-Harris of an affront to free speech and of treating UK universities like "Chinese re-education camps".
McCarthyism refers to US Senator Joseph McCarthy who led attempts to purge alleged Communists in public life the 1950s.