Ghaith, who is married to Fatima bin Laden and is an al-Qaida propagandist, hardly spoke beyond one-word replies to questions from the judge during a 20-minute arraignment, The New York Times reported. His lawyer pleaded not guilty on his behalf.
Federal prosecutors asked that Ghaith remain in custody. His lawyer did not object, but left open the possibility of seeking bail later, the Times said.
Prosecutors said Ghaith was captured Feb. 28 in Amman, Jordan, and brought to the United States the following day.
They told the court he answered questions from U.S. interrogators after he was taken into custody, giving a 22-page statement, the Times said.
Asked why Ghaith was being tried in a civilian court instead of a military setting, White House deputy press secretary Josh Earnest said the consensus among the appropriate departments and intelligence agencies was "the best way to protect our national security interests is to prosecute [Ghaith] in [a civilian] court."
Earnest noted that Faisal Shahzad, the Times Square bomber, and Umar Abdulmutallab, known as the underwear bomber because he tried to blow up a plane with explosives hidden in his underwear, were tried and sentenced to life in prison in civilian courts.
Civilian courts are "a more efficient way for us to deliver justice to those who seek to harm the United States of America," he said, adding Obama's national security team and federal agencies agreed it is "the best way to handle bringing ... Ghaith to justice."
Earnest said he didn't know whether anyone from the Obama administration spoke with New York Mayor Michael Bloomberg.
Some lawmakers expressed surprise by the events, accusing the Obama administration of dodging Congress, NBC News reported. They said Ghaith should have been taken to the U.S. military prison at Guantanamo Bay, Cuba, rather than the federal court in New York.
"Rather than issuing doomsday predictions about sequestration, the president should be notifying Congress that he's planning a U.S. civilian court trial for a terrorist who took credit for 9/11 and is on video threatening to blow up more U.S. buildings and planes," Sen. John Cornyn, R-Texas, said Friday. "Gitmo is still up and running. And as long as it is, it's the only place where we should be detaining America's most dangerous enemy combatants, period."
Justice Department officials said they don't think Ghaith had an operational role in al-Qaida for years and did not participate in any plot against the United States, including the Sept. 11, 2001, terrorist attacks, the Times said.
One law enforcement official said Ghaith was the most senior figure in the terror network to face a criminal trial in New York since America's war against al-Qaida began.
Officials said Ghaith, 47, originally was arrested in Turkey for entering the country illegally with a phony passport. Turkey was returning him to his home country of Kuwait when, during a stopover in Amman, U.S. officials took him into custody.
The operation in Jordon was a joint effort between the CIA and Jordan's spy service, the General Intelligence Directorate, officials said.
The White House and the CIA declined to comment, the Times said.
Among other things, the indictment indicated Ghaith appeared with al-Qaida founder bin Laden, who was killed in a U.S. raid in Pakistan in 2011, and Ayman al-Zawahri, a bin Laden deputy, and warned "a great army is gathering against" the United States and its allies. He also called upon "the nation of Islam" to do battle against "the Jews, the Christians and the Americans."