The terrorism suspect who had been undergoing interrogation on a Navy ship after his recent capture in Libya was brought to New York over the weekend and was to appear before a federal judge on Tuesday, officials said.
The decision to bring the suspect, Nazih Abdul-Hamed al-Ruqai, to New York was made because his chronic health problems worsened after he stopped eating and drinking aboard the San Antonio, a Navy vessel in the Mediterranean, officials said.
Mr. Ruqai, 49, was formally arrested and taken into Justice Department custody after he left the San Antonio and before he arrived in the United States late Saturday, officials said. Upon his arrival, he was taken to a medical facility, they said, and his condition has improved.
In 2000, Mr. Ruqai was indicted in Manhattan on charges that he conspired with Osama bin Laden in plots to attack United States forces in Saudi Arabia, Yemen and Somalia, as well as in the 1998 bombings of two United States Embassies in East Africa that killed 224 people.
His capture this month was seen as a potential intelligence coup because he had been on the run for years and so would, presumably, possess information about Al Qaeda from its earliest days through its contemporary, more scattered state.
Officials said that Mr. Ruqai, known as Abu Anas al-Libi, had been cooperating with the interrogation since his capture on Oct. 5. The decision to move him into the criminal justice system would not prevent prosecutors from seeking additional cooperation. But when he appears in Federal District Court on Tuesday, he will be appointed a lawyer, through whom the government will have to work if it wants to communicate further with him.
Preet Bharara, the United States attorney for the Southern District of New York, announced Mr. Ruqai’s arrival in a brief statement on Monday. Mr. Bharara’s office also wrote to Judge Lewis A. Kaplan, who has been overseeing the conspiracy cases in which Mr. Ruqai and other terrorism defendants have been charged, notifying him of the arrest and of Mr. Ruqai’s coming court appearance.
The handling of Mr. Ruqai since his capture has prompted a flare-up in the recurring debate about whether terrorism cases are better handled as military or civilian matters. The Obama administration has drawn fire for its hybrid approach, starting with interrogation in military custody and moving to prosecution in the traditional court system. The announcement on Monday of Mr. Ruqai’s abrupt transfer from one system to the other led voices on both sides of the debate to reprise their arguments.
Senator Patrick J. Leahy, Democrat of Vermont and chairman of the Senate Judiciary Committee, said the decision to move Mr. Ruqai into the civilian court system, rather than send him to the United States’ military prison at Guantánamo Bay, Cuba, showed that "the United States acts out of strength and not out of fear."
"We are not afraid of terrorists, nor are we afraid to bring them to justice in our courts," he said. "The indefinite detention of al-Libi at Guantánamo would have been unnecessary and unwise."
Representative Peter T. King, Republican of New York and a member of the House Intelligence Committee, said that he did not doubt the government’s explanation of the sudden turn of events involving a prized Qaeda suspect, and that it underscored his criticism of the Obama administration for not transferring Mr. Ruqai to Guantánamo immediately.
Mr. King said in a telephone interview that Mr. Ruqai’s move to a medical facility because of "some pre-existing condition" dispelled any notion that he had been injured in the raid in which he was captured in Tripoli, Libya, or during his interrogation.
But if his transfer into civilian custody means that Mr. Ruqai’s cooperation will now end, Mr. King said, that would amount to a major lost opportunity to obtain valuable intelligence.
"He was close to the top and an integral part of the Al Qaeda operation," Mr. King said. "After so much effort to take him alive, this is very unfortunate."
Details of the interrogation and of Mr. Ruqai’s statements are unknown. At first, when he was taken aboard the San Antonio, he ate and drank the provisions given to him, officials said. But as his health worsened in recent days, military doctors recommended that he be taken to a facility on land for better treatment.
Mr. Ruqai’s 20-year-old son, Abdullah, said in an interview the day after Mr. Ruqai was captured that his father suffered from a strain of hepatitis, and he expressed concern that his father was sick when he was detained.
Last week, during the interrogation, David E. Patton, the chief federal public defender in New York City, asked Judge Kaplan to appoint a lawyer to represent Mr. Ruqai, suggesting that such a proceeding could be conducted by videoconference.
Mr. Patton argued that Mr. Ruqai was entitled under federal rules to be taken "without unnecessary delay" before a magistrate judge, where he would have a right to counsel. Prosecutors objected, arguing that the request was premature because Mr. Ruqai had not yet been "criminally arrested," but had, rather, been detained by the "United States Armed Forces, acting under their own legal authorities."
On Friday, Judge Kaplan denied Mr. Patton’s request. Mr. Patton declined to comment.