Tory MP Chris Heaton-Harris "should probably not have sent" a letter to universities asking for details of Brexit courses, a minister has said.
Universities minister Jo Johnson said his colleague, a government whip, was "regretting very much" his decision,
He said the MP was "pursuing inquiries of his own" which may lead to a book on "the evolution of attitudes" to Europe rather than acting for the government.
Universities enjoyed "24 carat academic freedom" in the UK, he insisted.
Lecturers reacted with anger to the letter, calling it a "sinister" attempt to censor them and accusing Mr Heaton-Harris of conducting a "McCarthyite" witch hunt.
Downing Street distanced itself from the letter by Mr Heaton-Harris, a member of the European Research Group of Tory MP, after he wrote to universities asking for the names of professors teaching Brexit-related courses and details of their syllabuses.
Mr Heaton-Harris has not said himself what his intentions were, but said he believed in "open" debate about the UK's departure from the EU.
Speaking on BBC Radio 4's Today Mr Johnson, who said he had spoken to Mr Heaton-Harris, said: "Chris was acting in an individual capacity as an MP rather than as a government minister… Chris has a very longstanding interest in European affairs and the history of European thought.
"He was pursuing inquiries of his own which may, in time, lead to a book on these questions. It was more of an academic inquiry rather than an attempt to constrain the freedom that academics rightly have."
Asked if the letter should have been sent, he said Mr Heaton-Harris "probably didn't appreciate the degree to which this would be misinterpreted".
He said: "I am sure Chris is regretting this very much. The critical thing is that the government is absolutely committed to academic freedom and to freedom of speech in our universities.
"A letter which could have been misinterpreted should probably not have been sent."