Nazih Abdul-Hamed al-Ruqai, also known as Abu Anas al-Libi, had been interrogated without a lawyer on the USS San Antonio Navy ship.
But he was flown to New York when chronic health problems worsened after he stopped eating and drinking, officials said.
"He has several chronic, pre-existing health conditions," a U.S. official told The Washington Post. "The extent only became clear after his capture."
Ruqai's wife, Umm Abdul Rahman, told CNN her husband was infected with hepatitis C, which damages the liver.
Ruqai, 49, was arrested and placed in Justice Department custody after he left the San Antonio and before he arrived in New York late Saturday, officials said in announcing Ruqai's U.S. arrival Monday.
He was taken on arrival in New York to a medical facility, they said. His condition has improved, The New York Times reported.
Ruqai, who speaks Arabic and English, will be appointed a lawyer when he appears in U.S. District Court in lower Manhattan, officials said.
The government will then have to work through the lawyer if it wants to communicate further with him.
Ruqai was captured Oct. 5 in his native Tripoli, Libya, by U.S. Army Delta Force operators who caught him as he was returning home from morning prayers.
He was indicted in New York in 2000 on charges of conspiring with Osama bin Laden in plots to attack U.S. forces in Saudi Arabia, Yemen and Somalia. He was also indicated in the 1998 U.S. Embassy bombings in Nairobi, Kenya, and Dar es Salaam, Tanzania, which killed 224 people, including 12 Americans.
Rahman told CNN Oct. 7 her husband was innocent of the U.S. accusations and said he left al-Qaida in 1996, two years before the embassy bombings.
"I am sure of what I am saying -- he did not take part in any bombing anywhere in the world," Rahman said. "He participated in the jihad in Afghanistan. ... He was a member of al-Qaida and he was personal security for bin Laden -- that's true -- but he did not take part in any operation."
Four of Ruqai's co-defendants were convicted of carrying out the embassy bombings in a 2001 trial in New York. All were sentenced to life in prison.
Ruqai returned to his native Libya in 2011 to participate in the revolt against Moammar Gadhafi.
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