The bill, published on Wednesday, coincides with the publication of the report on the murder of Lee Rigby in Woolwich last year
A spokesman for Universities UK said: "The sector has engaged extensively with the government's Prevent agenda and there are strong partnerships with the police and security services."
Amnesty International UK legal adviser, Rachel Logan, raised concerns over some of the powers in the legislation.
She said: "It's dangerous to rush through this grab-bag of measures without proper scrutiny or challenge.
"While the Government needs to ensure that anyone suspected of criminal activity is investigated, measures like invalidating passports and excluding British nationals from their home country push the boundaries of international law.
"Meanwhile, adding the internal exile of forced relocation to the already unfair Tpims regime is another measure which causes significant concern for basic freedoms. We simply don't have the fair and proper processes in place for such drastic decisions."
Islamic Human Rights Commission chair Massoud Shadjareh added: "To go down the same route of policies which have failed to address terrorism is just going to alienate Muslims further and increase 'otherisation' of communities, encouraging the kind of victimisation that has resulted in ever-increasing attacks on places of worship and individuals."