Known as one of al-Qaida's early computer experts, he is accused of helping plan and conduct surveillance for the attacks. He is believed to have used an early-generation Apple computer to assemble surveillance photographs.
The defendant kept his hands folded on his lap as the judge read the charges in a courtroom secured by about a dozen deputy U.S. marshals. The judge ordered him detained after a federal prosecutor called him a "clear danger."
Republicans stepped up their criticism of Obama for his administration's handling of the defendant, saying he should have been sent to the American prison at Guantanamo Bay for more interrogation instead of being taken to the U.S. and given access to civilian courts and the legal protections they provide.
"He was a treasure trove of information," said Sen. Lindsey Graham.
"The most dangerous thing we could do as a nation is to treat a captured al-Qaida terrorist as a common criminal, read them their Miranda rights and put them in civilian court before we have a chance to gather intelligence."
Rep. Peter King, a member of the House Intelligence Committee, said: "The real issue is the intelligence. Once he gets a lawyer, he holds the cards. ... Put it this way: Now he decides whether he will talk."
Democratic Sen. Patrick Leahy defended the administration, saying dozens of terrorists have been arrested and continued providing information.
"Wouldn't it be nice if we demonstrated to the rest of the world that we're not afraid of these people, that we have the best court systems in the world and we're going to use them?" he said.
Al-Libi's family and former associates have denied he was ever a member of al-Qaida.
"The presumption of innocence is not a small technicality here," his court-appointed attorney, David Patton, said in email sent after the hearing. In a 150-page indictment, al-Libi "is mentioned in a mere three paragraphs relating to conduct in 1993 and 1994 and nothing since. ... There is no allegation that he had any connection to al-Qaida after 1994, and he is eager to move forward with the legal process in this case."
The defendant's lawyers said his given name is Nazih Abdul-Hamed al-Ruqai. Al-Libi, they said, was an old alias meaning "The Libyan," a version of which was used in the original indictment. Federal authorities continued to call him al-Libi while he was wanted as a fugitive, but they didn't put a fight Tuesday when he told the judge the name he wants to go by in court is al-Ruqai.
The prosecution in the United States is in keeping with a policy of bringing suspected al-Qaida sympathizers and operatives to civilian courts rather than military tribunals.
The civilian court prosecutions have continued before and after the Obama administration was forced to reverse its plans to prosecute 9/11 mastermind Khalid Sheikh Mohammed and several others in federal court in Manhattan.
Before the Sept. 11 attacks, several other major terrorism trials were held in New York, including those of blind Egyptian sheik Omar Abdel-Rahman and Ramzi Yousef, who was the architect of the 1993 World Trade Center bombing.
Just weeks before 9/11, four men were convicted in the embassy bombings and were sentenced to life in prison, two of them after a jury rejected the death penalty.
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Associated Press writers Bradley Klapper and Eileen Sullivan in Washington and Frank Eltman on Long Island contributed to this report.
