Communities Secretary Eric Pickles believes the University and College Union's rejection of the widely-accepted definition of antisemitism sends a "chilling message" to Jewish academics and students.
Writing exclusively for the JC, Mr Pickles says UCU now believes that Jews are "fair game for invective" and has become "a most unlikely champion of free speech".
"It has been boycotting visits by Israeli academics for a number of years. Their actions suggest that their true goal is not and cannot be to secure freedom of speech, but to silence dissenting opinion."
Jewish community leaders reacted with outrage when delegates at May's UCU annual congress overwhelmingly supported the executive's resolution distancing the organisation from the European Union's working definition on antisemitism.
UCU claimed the definition prevented the full and open discussion of Israel and Palestine on campus.
Mr Pickles also cites UCU's 2006 rejection of the All-Party Parliamentary Inquiry into Antisemitism's findings, and the Union's 2009 invitation to South African trade unionist Bongani Masuku - who had called for Jews in South Africa to be stripped of their citizenship – to speak at a conference.
Mr Pickles writes: "Seen in this context, the latest resolution is in fact sending out a chilling message. It says that Jewish academics and students who perceive that they are being harassed or bullied should understand that they will be held to a different standard. It says that they should expect to be fair game for invective, and learn to live with feeling more vulnerable.
"Little wonder that the Union has already seen many members of the Jewish faith, other faiths and none vote with their feet and leave."
Baroness Deech, a member of the
All-Party Parliamentary Group Against Antisemitism, welcomed Mr Pickles' remarks.
She said: "This is an appropriate and timely intervention. I am heartened by the seriousness with which he is addressing the actions of the UCU. This gives me some hope that the UCU will be forced to change.
"Like the Secretary of State, I have asked the Equality and Human Rights Commission to investigate the UCU's apparent institutional racism. It is simply not acceptable that Jewish students and lecturers are being denied rights that are available to others."
UCU general secretary Sally Hunt was unavailable to respond to Mr Pickles's comments.