Under the rules of war, al-Libi could only be held for up to 60 days aboard the Navy ship before being handed over to federal law enforcement.
Members of 1st Special Forces Operational Detachment-Delta, known as Delta Force, took al-Libi during a daylight capture mission in Tripoli.
The senior al Qaeda leader was indicted in absentia for his role in the bombings of the United States embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya, in 1998.
Al-Libi's limited interrogation by U.S. officials and President Obama's decision to try him in civilian court has riled congressional Republicans.
Republican lawmakers claim Obama is putting politics ahead of national security by refusing to send al-Libi to the military prison in Guantánamo Bay, Cuba.
“In criminal [court] you are trying to solve a crime — in war you are trying to defeat the enemy,” Sen. Lindsey Graham (R-S.C.) said shortly after al-Libi's capture.
Obama administration officials are pressing ahead with the president's plan to shutter the controversial detention center in Cuba by the end of his presidency.
Sen. Kelly Ayotte (R-N.H.) said it would be “absolutely unacceptable” if the chance to interrogate al-Libi were sacrificed in pursuit of Obama’s first-term promise to close the prison.
“Our nation deserves better,” she said at the time.
During his Senate confirmation hearing last Thursday, Obama nominee Michael Lumpkin raised concerns over how the White House is handling al-Libi's detention and interrogation.
"Whenever we can capture somebody of that stature, the intelligence we can and will gain is significant, that can lead to future operations and ultimately save Americans' lives," Lumpkin told the Senate Armed Services Committee.
If confirmed, Lumpkin would officially become the Pentagon's chief of special operations and low-intensity conflict.
Lumpkin said the "preferred methodology" would not to cap interrogations of terror suspects, particularly a senior al Qaeda leader like al-Libi.
"From an operational standpoint, that's the preferred methodology," Lumpkin said.
"As things flow ... you don't know necessarily what you're going to get, and you don't want to be up against a clock," he added.
During the hearing, Lumpkin made clear to Ayotte his office had no involvement or insight into the al-Libi operation and ongoing interrogation.
"On these particular operations, I can provide no granularity or fidelity," the nominee told Ayotte.
That said, "I'm always hesitant on time lines," Lumpkin added.