A U.S. citizen, believed to have trained with al-Qaeda in Pakistan, is set to face terrorism charges in New York. (Reuters)

An American citizen who was once thought to be a top operative in al-Qaeda has been detained in Pakistan and secretly flown to New York to face federal terrorism charges, according to U.S. officials.

Muhanad Mahmoud al Farekh, 29, did not enter a plea during a brief arraignment in federal court in Brooklyn on Thursday. Farekh, also known by the nom de guerre Abdullah al-Shami, was charged with conspiracy to provide material support to terrorists. A judge ordered him held.

Pakistani forces detained Farekh several weeks ago and recently transferred him to U.S. custody after his identity was confirmed. Officials said he was questioned by members of an interrogation team composed of FBI, CIA and Pentagon officials and then advised of his Miranda rights.

Little is known about Farekh, who is believed to have been born in Texas but to have moved with his family at a young age to Jordan, where he also has citizenship. He also attended school in Canada.

He and two other associates were studying at the University of Manitoba when, around 2007, they sold their belongings and left Winnepeg. They then traveled to Pakistan to link up with militants and fight against American forces, according to a criminal complaint filed in the Eastern District of New York.

The three called a friend in Canada when they arrived and told him they intended to become “martyrs,” the complaint says.

Over the next several years, Farekh rose through al-Qaeda’s ranks, later coming to the attention of U.S. intelligence officials. By 2013, he had been nominated by the Pentagon to a “kill list” of suspected terrorists.

Senior U.S. officials said consideration of that nomination stalled as the Justice Department examined whether it would be legal to kill him, given his American citizenship. The Obama administration had previously authorized the killing of Anwar al-Awlaki, a radical American-born cleric in Yemen who was determined to have presented a continuing and imminent threat to U.S. interests and who could not feasibly be captured.

Officials said there were questions about how prominent a role Farekh played in al-Qaeda. The decision not to authorize his killing frustrated members of Congress who thought the administration was dithering, officials said.

If convicted, Farekh faces a maximum of 15 years in prison.

He is the second terrorism suspect with U.S. ties to be captured or killed in Pakistan in recent months. In December, Pakistani forces killed Adnan el Shukrijumah, a senior al-Qaeda operative on the FBI’s Most Wanted Terrorists list. Shukrijumah had been indicted in New York on charges that he played a role in the terrorist group’s failed plan to attack the city’s subways in 2009.

The move to bring Farekh to the United States to face federal charges is likely to draw criticism from some Republicans in Congress who believe suspected terrorists, even Americans, should not have the same rights as criminal defendants and should be held at the prison at Guantanamo Bay, Cuba.

President Obama, however, has vowed to close the facility, and no detainee has been sent there since 2008.

The federal prosecution of terrorism suspects captured overseas has become almost commonplace. Last year, a Russian citizen who was captured in Afghanistan and held there for years was indicted in U.S. federal court and charged with conspiring to murder a U.S. national and with use of a weapon of mass destruction. That case marked the first time a foreign combatant captured on the battlefield in Afghanistan had been brought to the United States to be prosecuted.

The FBI’s Joint Terrorism Task Force in New York, working with federal prosecutors there, handled the case against Farekh. One of the officials briefed on the case said Farekh was interrogated at length by what is known as a High-Value Detainee Interrogation Group.

“Today’s arrest demonstrates that there is no escape from the long reach of our law for American citizens who seek to do harm to our country on behalf of violent terrorists,” said U.S. Attorney Loretta E. Lynch. “We will continue to use every tool at our disposal to bring such individuals to justice.”

It is not clear where the interrogations of Farekh took place. In the past, officials have used Bagram air base in Afghanistan or warships to question terrorism suspects who were later brought to the United States.

Farekh’s capture comes after Pakistan began a long-promised military offensive against militant forces lodged in North Waziristan, part of the tribal areas along the Afghanistan border that are used as safe havens by terrorist groups.

Pakistan claimed to have killed nearly 1,000 militants as part of the offensive.

In operations in North Waziristan and nearby regions, as well as in Karachi, Pakistani forces say they have also killed and captured numerous al-Qaeda operatives, including Shukrijumah, who was born in Saudi Arabia and was believed to have been in charge of the group’s external operations.

Craig reported from Islamabad. Karen DeYoung and Sari Horwitz in Washington contributed to this report.