BERLIN — The authorities in Hamburg said Monday that they had shut down the mosque where several of the hijackers involved in the Sept. 11 attacks had met, asserting that it remained a source of radicalization nearly a decade later.

The Masjid Taiba mosque in Hamburg, known at the time of the hijackings in 2001 as Al Quds mosque, was “closed effective immediately,” according to a statement by the Hamburg Interior Ministry. German television showed blue-uniformed police officers carrying computers out of the mosque in the St. Georg neighborhood.

That the small mosque near Hamburg’s main train station was still in operation and still, according to law enforcement officials, indoctrinating young people with a form of Islam that encouraged violence demonstrated the challenges faced by Western democracies like Germany in controlling extremism without impinging on civil rights and religious freedom.

The mosque had been under surveillance for years, but efforts to close it received new urgency after a group of radicalized young people associated with the mosque, most of them German citizens with roots in Muslim countries, traveled last year to the region along the border shared by Afghanistan and Pakistan. Officials said clearing the legal and bureaucratic obstacles to closing a mosque was a slow process, one that finally succeeded Monday.

German intelligence officials have expressed concerns over the growing number of young Germans drawn into militant Islam and the possibility that they could return from the Pakistan-Afghanistan border region to commit acts of terror.

“Today we closed the Taiba mosque because young men were being turned into religious fanatics there,” said Christoph Ahlhaus, secretary of the interior for the city of Hamburg, at a news conference. “Behind the scenes, a supposed cultural organization shamelessly used the freedoms of our democratic rule of law to promote holy war.”

Mr. Ahlhaus said, “Hamburg cannot become a cradle for Islamists capable of violence.”

Police officers searched the mosque and the apartments of leading mosque members starting at 6 a.m., and seized their assets. The door to the mosque was sealed after the searches, and the group’s Web site yielded only an error message on Monday. The authorities also banned the cultural association that ran the mosque, which was founded in 1993. The name of the mosque was changed from Al Quds to Masjid Taiba in 2008.

The mosque achieved worldwide notoriety after the attacks on Sept. 11, 2001. Mohamed Atta, Marwan al-Shehhi and other members of the group that carried out the attacks had used the mosque as a meeting place.

A report released in May by the Interior Ministry said that the mosque “remains the central attraction for the jihadist scene.” According to the report, a group of 11 people who met at the mosque traveled from Hamburg to the region along the Pakistan-Afghanistan border in March 2009, probably with the goal of training at a militant camp there. One of the 11 was detained in Pakistan and sent back to Germany.

Another member of the group joined the Islamic Movement of Uzbekistan, described by German law enforcement officials as a terrorist group, and appeared in a German-language propaganda video calling for Muslims to join in holy war.

The current imam at the mosque, Mamoun Darkazanli, a German of Syrian origin, was suspected by Spanish authorities of having provided logistical and financial support to Al Qaeda. He was arrested in 2004, but Germany’s highest court refused in 2005 to turn him over to Spain, arguing that a European agreement to streamline extradition procedures violated the rights of German citizens.

German prosecutors ended their investigation into Mr. Darkazanli because of lack of evidence. Mr. Darkazanli’s whereabouts and response to the mosque closing were not clear on Monday. No one answered the telephone at the mosque, and Mr. Darkazanli could not be reached for comment.

A spokesman for the Interior Ministry, Ralf Kunz, said that the mosque had been under observation since 2001, but that the investigation intensified after the group’s trip last year. But in order to satisfy the requirements for banning an organization, particularly a religious one, “intelligence work was necessary, and that can take time,” Mr. Kunz said.

“We gathered enough material that the court ruled we could perform our searches there and that we could ban the organization,” he said.

But the mosque’s closing was also criticized. “The decision to close the mosque poses a serious threat and was counterproductive,” said Norbert Müller, a member of the board of the Schura Association of Islamic Communities in Hamburg.

Mr. Müller said that the small mosque was isolated, making it relatively easy for the police to keep tabs on its congregation’s movements and activities. Closing the mosque only scattered the radical elements; “it doesn’t get rid of them,” Mr. Müller said.