The fugitive, known by the alias Anas al-Liby, is in military custody on the USS San Antonio and is being interrogated for intelligence purposes without a lawyer present, the officials told The New York Times.
The 49-year-old Libyan national, who has used several aliases, is eventually expected to be sent to New York for criminal prosecution, the officials told the newspaper.
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 indicted in the 1998 U.S. Embassy bombings in Nairobi, Kenya, and Dar es Salaam, Tanzania, which killed 224 people.
The Defense Department had no immediate comment on the Times report.
The department said Sunday al-Liby -- whose birth name is Nazih Abdul-Hamed al-Ruqai -- was "currently lawfully detained under the law of war in a secure location outside of Libya."
"Wherever possible, our first priority is and always has been to apprehend terrorist suspects, and to preserve the opportunity to elicit valuable intelligence that can help us protect the American people," the statement said.
Al-Liby is seen as a potential intelligence gold mine, the Times said, because he may have two decades of information about al-Qaida, from its earliest days.
Al-Liby was captured Saturday by the U.S. Army's Delta Force, assisted by FBI and CIA agents.
Navy SEALs, meanwhile, carried out an unsuccessful simultaneous raid in Somalia to capture a reputed senior al-Shabaab militant Islamist group leader, linked to al-Qaida, who was the alleged mastermind behind the massacre at the Westgate shopping mall in Nairobi, Kenya, two weeks ago. U.S. Navy SEAL Team Six withdrew from capturing suspected terrorist leader Ikrima when it became clear he could not be taken alive in Somalia, an official said.
"Their mission was to capture him. Once it became clear we were not going to take him, the Navy commander made the decision to withdraw," an unidentified U.S. official told CNN of the plan to capture Ikrima, an al-Shabaab leader considered responsible for bombings in East Africa.
The official said U.S. forces withdrew from fighting during the weekend after the SEALs came under heavy fire, and the mission's aim, to capture Ikrima alive, was the reason troops were deployed instead of a drone attack.