The Most Rev Justin Welby told ministers at Westminster that "mere exhortation" was not working.
The leading Anglican made the intervention as peers heard just five universities were known to have adopted an agreed definition of anti-Semitism.
The archbishop, who is President of the Council of Christians and Jews (CCJ), said: "We hear numerous reports of no-platforming, of intimidation and lack of free speech.
"I accept fully that the universities are autonomous but will the minister look for ways in which pressure can be applied to ensure these standards are kept?
"Because mere exhortation, would she agree, is not really working."
Government frontbencher Baroness Berridge pointed out the Lords has legislated to ensure the independence of universities.
She said: "Although the secretary of state can issue guidance, that guidance has to take into account the autonomy of our academic institutions."
Lady Berridge told peers the Government "strongly encourages" higher education institutions to adopt the International Holocaust Remembrance Alliance's definition of antisemitism.
Responding to a question in the House of Lords, Lady Berridge said only five providers had informed the Government that they had adopted the definition.
She said: "As autonomous institutions, the decision rests with individual providers.
"But the Government will continue to urge and encourage them to adopt this important definition."
Tory peer Lord Leigh of Hurley, who is vice president of the Jewish Leadership Council, said it was "very disappointing" so few institutions had agreed to adopt the definition.
Lady Berridge said: "Yes it is disappointing, but the Government is only aware of five institutions. There may be other providers."
Referring to the freedom of expression code for universities, drawn up by the Equality and Human Rights Commission (EHRC), Lady Berridge said: "Universities should be in no doubt now between their duty to promote free speech and the holding of events on campuses."
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