Tariq Ramadan, a Swiss citizen who now teaches at Oxford University in the UK, had his US visa revoked in 2004, shortly before he was scheduled to move to the US to accept a position at the University of Notre Dame in Indiana.
The American Civil Liberties Union (ACLU), which is representing Ramadan, said the State Department excluded the professor under a provision of the Patriot Act that allows the government to bar entry to any prominent foreigner who has used his status to endorse or espouse terrorism.
Ramadan is a critic of the US invasion of Iraq and has said he sympathises with nonviolent Palestinian resistance against Israel, but says he is a moderate who opposes terrorism and does not support Islamic extremism.
"It would be absurd to suggest that this criticism - the same kind of criticism that appears every morning in the editorial pages of major American newspapers - amounts to approval of terrorism," the ACLU lawsuit said on Wednesday.
Jameel Jaffer, an ACLU lawyer, added: "The government doesn't have the authority to exclude people from the country, invited scholars, simply because it doesn't like what they have to say."
US officials have yet to publicly detail their reasons for revoking Ramadan's visa.
The professor has long drawn extra attention because he is the grandson of Hassan al-Banna, who founded the Muslim Brotherhood, the largest Muslim revivalist group in Egypt.
US Justice Department legal officials have yet to file papers responding to the lawsuit.