Facing a court-ordered deadline, the State Department has rejected a visa application from a prominent Muslim scholar who was granted a tenured position at the University of Notre Dame in 2004 but never assumed the post because he was denied entry to America.

In June, a federal judge gave the government 90 days to grant a visa to the Swiss-born author and lecturer, Tariq Ramadan, or explain why it would not. Last week, Mr. Ramadan received a letter indicating that his new visa application was denied because of 600 euros (now worth about $765) in donations he made to groups in France and Switzerland alleged to have links to a Palestinian Arab terrorist group, Hamas.

“A U.S.consular officer has denied Dr. Tariq Ramadan’s visa application,” a spokesman for the State Department, Kurtis Cooper, said. “The consular officer concluded that Dr. Ramadan was inadmissible based solely on his actions, which constituted providing material support to a terrorist organization.”

Mr. Ramadan, 44, who has been teaching at Oxford, said yesterday that he doubted the donations were the real reason for barring him from America. It is “clear from the history of this case that the U.S. government’s real fear is of my ideas,” the Muslim scholar said in a statement posted on his Web site. “I am excluded not because the government truly believes me to be a national security threat but because of my criticisms of American foreign policies in the Middle East; because of my opposition to the invasion of Iraq; and because of my criticism of some of the Bush administration’s policies with respect to civil liberties.”

An American Civil Liberties Union attorney who led Mr. Ramadan’s lawsuit, Jameel Jaffer, said further court action is possible. “It’s not a good enough answer,” Mr. Jaffer said. “Our belief is the new reason is pretextual.”

Prior to 2004, Mr. Ramadan was a frequent visitor to America, attending conferences organized by major universities such as Harvard and Stanford, and one public discussion on Islam arranged by President Clinton’s foundation.

Mr. Ramadan, who is referred to by some as the Muslim Martin Luther, was named by Time magazine as one of the 100 most influential scientists and thinkers in the world. However, he has been dogged by allegations that his writings and speeches excuse or justify terrorism. Mr. Ramadan has repeatedly expressed opposition to terrorism, but several Islamic extremists jailed for terrorist activities have claimed inspiration from the Muslim scholar. When Mr. Ramadan was awarded the Notre Dame faculty position, the State Department issued him a work visa. However, in July 2004, the visa was revoked after the government said it received new information about Mr. Ramadan. A spokesman for the Department of Homeland Security, Russell Knocke, said at the time that the scholar was being excluded under a legal provision targeting those who have used a “position of prominence within any country to endorse or espouse terrorist activity.”

Mr. Ramadan said yesterday that the government has now retreated from that claim. “I am glad that the State Department has abandoned its allegation that I endorse terrorism,” he said.

Mr. Cooper declined to identify the groups that received the donations that allegedly led to the visa denial. A statement posted on Mr. Ramadan’s Web site did not name them, but described them as “humanitarian organizations” which are legal in Europe but have been banned from fund-raising in America. “The U.S. government apparently believes that the organizations to which I gave small amounts of money have in turn given money to Hamas,” he wrote.

A New York Sun review of sanctions lists issued by the Treasury Department quickly identified the groups as the Paris-based Comité de Bienfaisance et Secours aux Palestiniens, and Association de Secours Palestinien, based in Basel, Switzerland. The organizations were blacklisted by American authorities in August 2003, days after Hamas claimed responsibility for a bomb attack that killed 23 passengers on a Jerusalem bus. A spokesman for the French group was not available yesterday. The Swiss office appears to have closed.

Mr. Jaffer said Mr. Ramadan is unsure whether any of his gifts came after America banned financial dealings with the groups. “His intent was to support humanitarian work in the Palestinian territories. He’s not ashamed of that,” the attorney said. Mr. Jaffer said he believes that the government was unaware of the donations until Mr. Ramadan told a consular official about them in an interview in December 2005.

A Jewish leader in Switzerland told the Sun that there was circumstantial evidence that Mr. Ramadan’s ties to the Paris-based Palestinian Arab group could extend beyond charitable donations. The secretary-general of the Coordination Intercommunautaire Contre L’Antisemitisme et la Diffamation, Johanne Gurfinkiel, said a publishing house used by the Muslim scholar was located in the same building in Lyon as the fund-raising committee allegedly linked to Hamas.”We were just wondering what they were doing together at the same address, nearly,” Mr. Gurfinkiel said.

Mr. Gurfinkiel said the Palestinian Arab committees in France and Switzerland seemed to be vehicles for funding terrorists, but he said he was dubious that relatively small gifts justified barring Mr. Ramadan from America. “I don’t know if it’s a very good argument to say, ‘He gave 600 euros. We won’t give him a visa,'” Mr. Gurfinkiel said.