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The appearance of Mr. Abu Ghaith before Judge Lewis A. Kaplan of United States District Court in the cavernous ceremonial courtroom in Lower Manhattan, only blocks from the site of the 9/11 terror attack, was fraught with symbolism, even as the details of both his role in Al Qaeda and his arrest remained unclear.

Mr. Abu Ghaith, a slight, trim man with a manicured gray beard and dressed in a blue prison smock, barely spoke aside from some one-word replies to questions from the judge during the 20-minute arraignment. His lawyer pleaded not guilty on his behalf.

Federal prosecutors asked that Mr. Abu Ghaith remain in custody. His lawyer did not challenge the request, but left open the possibility of making a bail application later.

Justice Department officials described Mr. Abu Ghaith as a propagandist who they believe has not had an operational role in Al Qaeda for years and did not participate in the attacks on Sept. 11, 2001, or in any plots against the United States.

But one law enforcement official said that Mr. Abu Ghaith, 47, was the most senior Qaeda figure to face criminal trial in New York since America's war against the terrorist network began. He was married to one of Bin Laden's daughters, Fatima, and the indictment alleges a working relationship with the terrorist group's leader, who was killed by United States forces in Pakistan in 2011.

"Among other things, Abu Ghaith urged others to swear allegiance to Bin Laden, spoke on behalf of and in support of Al Qaeda's mission, and warned that attacks similar to those of Sept. 11, 2001 would continue," according to the indictment.

John P. Cronan, one of the prosecutors, told Judge Kaplan that Mr. Abu Ghaith made extensive comments to law enforcement officials after his arrest. He referred to a 22–page document, which was not released publicly, that detailed his statements. Mr. Cronan also referred to audio recordings of statements Mr. Abu Ghaith made to foreign authorities, some of which he said still need to be translated.

The decision to hold Mr. Abu Ghaith's trial in the United States was criticized by some lawmakers who believe that he should not be afforded the privileges or platform that he will be accorded in a civilian court as opposed to a military tribunal.

Outside the courtroom, where dozens of news organizations stood vigil in the blustering wind and snow, there was a noticeable increase in security, with police officers patrolling the perimeter with bomb-sniffing dogs and extra barriers set up for crowd control.

Mayor Michael R. Bloomberg, speaking on his weekly radio show Friday morning, said he would not second-guess the decision to hold the trial in New York.

"No street is going to be closed because of this," he said. "Would I prefer to have it elsewheres? I'm not going to get involved in that because I don't want to make the president's job any more difficult."

Details about Mr. Abu Ghaith's arrest remained sketchy, but officials said he was originally detained last month while staying in a hotel in Ankara, Turkey, after crossing the border from Iran, where he had been living for about a decade. According to one person in Washington briefed on the matter, Turkish officials rebuffed demands by the Obama administration to directly hand him over to the United States, choosing instead to deport him to Kuwait, his home country. On a stopover in Amman, Jordan, American officials took him into custody and flew him to New York.

Jordan's spy service, the General Intelligence Directorate, is one of the Central Intelligence Agency's closest partners in the Middle East.

Mr. Abu Ghaith was a Muslim preacher and teacher in Kuwait who spoke out against Saddam Hussein's invasion of Kuwait in 1990. In 2000, he traveled to Afghanistan, where he met Bin Laden and eventually married one of his daughters. He attracted wide attention in the days after the Sept. 11 attacks by making statements defending the attacks, some of them carried on Al Jazeera.

According to an indictment unsealed Thursday, Mr. Abu Ghaith appeared with Bin Laden and Ayman al-Zawahri, who was then Bin Laden's deputy, and warned the United States and its allies that a "great army is gathering against you." He called upon "the nation of Islam" to do battle against "the Jews, the Christians and the Americans."

He also urged people at a guesthouse in Kandahar, Afghanistan, to swear allegiance to Bin Laden, and on the night of the World Trade Center and Pentagon attacks, Bin Laden summoned him and asked for his assistance, which he agreed to provide, according to the indictment.

Mr. Abu Ghaith's lawyer, Philip L. Weinstein, declined to comment before the arraignment.

The arrest of Mr. Abu Ghaith was the rare occasion in which a Qaeda operative was detained overseas rather than killed. The Obama administration has expanded the use of targeted killing operations in Pakistan, Yemen and elsewhere, asserting that they are justified when there is no possibility of capture.

Spokesmen for the C.I.A. and the White House declined to comment.

Mr. Abu Ghaith went to Iran in 2002, one of a few Qaeda operatives who traveled there in the months after the Sept. 11 attacks. Intelligence officials have long debated how the group of operatives — several who are members of Al Qaeda's "shura council" — has been treated inside Iran, and his trial could shed light on its members' lives there. Some officials described them as being under a kind of house arrest, and point out that Iran — a country run by a Shiite Muslim theocracy — would be wary of any alliance with Al Qaeda, a Sunni terrorist network. Others believe that Iran might at least be using the group to keep open communication channels with senior Qaeda leaders in Pakistan.

In recent months, American spy agencies have picked up indications that the Qaeda operatives inside Iran — including Saif al-Adel, an Egyptian who is the terrorist group's senior operative in Iran — might be trying to return to their home countries.

George Venizelos, the assistant director in charge of the New York F.B.I. office, compared Mr. Abu Ghaith's position in Al Qaeda to the consigliere in a mob family, or propaganda minister in a totalitarian regime. He said Mr. Abu Ghaith used his role to persuade others to join "Al Qaeda's murderous cause."

Seth Jones, a terrorism expert at the RAND Corporation, said, "He had serious religious credibility inside of Al Qaeda." Mr. Jones said that it was unlikely that Mr. Abu Ghaith would have intelligence about any active Qaeda plots, but that he could be a useful source of information about the movement of the group's operatives through Iran.

In 2010, the Obama administration abandoned plans to bring five men charged with plotting the Sept. 11 attacks — including the accused mastermind, Khalid Shaikh Mohammed, a far more significant Qaeda figure — to trial in the same courthouse in Lower Manhattan where Mr. Abu Ghaith will appear Friday, blocks from the World Trade Center site.

The turnaround came in the face of nearly unanimous pressure from New York officials and business leaders after Mayor Bloomberg withdrew his initial support for the plan, saying the security costs and disruption would be too great. The police commissioner, Raymond W. Kelly, had outlined a plan for securing the trial that involved transforming a section of Lower Manhattan into an armed camp, blanketed with police checkpoints, vehicle searches, rooftop snipers and canine patrols. But should Mr. Abu Ghaith go to trial, officials said, the proceedings would most likely draw far less attention and create far fewer problems.

Three terrorism defendants, who were extradited from Britain in October, are already facing trial in Manhattan.

They include Abu Hamza al-Masri, the fiery Islamic preacher who has been charged with conspiring in a 1998 kidnapping of American and other tourists in Yemen and in trying to help establish a terrorist training camp in Oregon, and Adel Abdul Bary, charged with conspiring in the 1998 bombings of two United States Embassies in East Africa. Both have pleaded not guilty.

But the plan to put Mr. Abu Ghaith on trial in New York City drew immediate criticism.

Representative Mike Rogers, Republican of Michigan, the chairman of the House Select Intelligence Committee, said in a statement that Qaeda leaders captured on the battlefield should not be brought to the United States to stand trial. "We should treat enemy combatants like the enemy — the U.S. court system is not the appropriate venue. The president needs to send any captured Al Qaeda members to Guantánamo," he said.

Julie Menin, the former chairwoman of Community Board 1 in Lower Manhattan, who opposed the earlier plan to try senior Qaeda operatives in New York, said she was in favor of a Manhattan trial for Mr. Abu Ghaith.

"I think it is a very different situation," said Ms. Menin, who is running for Manhattan borough president and said her opposition to the earlier trial was based on the intense disruption that security precautions would have brought to the neighborhood.