"I cannot imagine that any vice-chancellor should be proud of the fact that vilification of a people has been taking place on their campus," he said.
Rabbi Mirvis, who leads Jewish people throughout the Commonwealth, has spoken out after growing concerns over "Zionist bashing" and "Jew hate".
He told the Sunday Times: "We have seen what Jew hatred can be a template for in history. What troubles me is that the Zionist bashing on campus has gone unchallenged.
"To vice-chancellors I would say: see what is happening under your noses, what is happening to the reputation of your universities."
Echoing the growing debate around safe spaces for debate on university campuses, Rabbi Mirvis said: "Freedom of speech needs to take place in a healthy and appropriate context."
Freedom of speech needs to take place in a healthy and appropriate context Chief Rabbi Ephraim Mirvis
Responding to fears Jewish students may leave British universities to study abroad, Mirvis said: “We are not running anywhere."
The student movement has been rocked by claims of anti-Semitism.
Oxford University's Labour society has been embroiled in allegations of racism, including specific anti-Semitic abuse.
Labour will launch an independent inquiry into claims of a wider problem with anti-Jewish sentiment in the party.
Bouattia said that to be anti-Zionist is not to be anti-Jewish.
The union's national conference sparked controversy after delegates heard speeches against commemorating the Jewish Holocaust, known as the Shoah.
What is Zionism?
Merriam-Webster defines Zionism as: "Political support for the creation and development of a Jewish homeland in Israel."
Encyclopedia Britannica defines Zionism as: "Jewish nationalist movement that has had as its goal the creation and support of a Jewish national state in Palestine, the ancient homeland of the Jews."
However, as Haaretz notes: "Over the past 20 to 30 years, this simple concept has turned into one of the most confused and complicated notions of identity, and its overuse has made it impossible to agree on what it means."
Imogen Wilson, a vice-president at Edinburgh Students' Association, wrote of safe space: "It is there to protect free speech, by making sure that everyone's voices and opinions are heard, and especially that students from marginalised groups feel comfortable contributing.
"It's the student union way of making politics more accessible, and trying to steer it away the 'old boys club' ways of the past - and it works.
"The underlying benefits of safe space come from people knowing that racist, ableist, homophobic, sexist, and transphobic language is unacceptable, and it leads to more constructive and respectful debate."