Tripoli demands answers from the US and wants to know why it was not told about the raid by American special forces on its soil.
Libya has condemned the capture of an al Qaeda leader linked to the 1998 American Embassy bombings in east Africa and wanted by the FBI for more than a decade.
The government said it wanted answers from the US over the “kidnap of a Libyan citizen” on its own soil and demanded to know why it was not told about the raid by American special forces.
Nazih Abdul-Hamed al Ruqai, known by his alias Anas al Libi, has been on America’s most wanted terrorists list since it was introduced after the September 11 attacks.
His capture represents a significant blow to what remains of the core al Qaeda terror network, once led by Osama bin Laden.
Libya underlined its “desire to see Libyan citizens tried in their own country” and pointed out that Tripoli and the US were bound by a “strategic partnership” that dealt with security and defence matters.
“The government hopes that this strategic partnership will not be damaged by this incident,” it said in a statement.
Earlier, US Secretary of State John Kerry, in Bali for an economic summit, hailed the Libya operation and Saturday’s failed mission to capture an al Shabaab leader in Somalia, and said terrorists “can run but they can’t hide”.
“We hope that this makes clear that the USA will never stop in the effort to hold those accountable who conduct acts of terror,” he said.
Family members said gunmen in a three-car convoy seized al Libi outside his home in the Libyan capital Tripoli.
His brother Nabih said the 49-year-old was parking on Saturday after dawn prayers, when three vehicles encircled his vehicle. The gunmen smashed his car window and seized his weapon before grabbing him and fleeing.
Al Libi’s wife saw the kidnapping from her window and described the abductors as foreign-looking armed “commandos”, he said.
US officials said there were no American casualties in the operation. Al Libi is thought to have spent time in Sudan, where bin Laden was based
Al Libi, who had a $5m (£3.1m) FBI bounty on his head, was charged by a US federal court for his alleged role in the 1998 bombings of the US embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya, that killed more than 220 people.
He is believed to have returned to Libya during the 2011 civil war that led to the toppling and killing of Colonel Muammar Gaddafi.
The alleged al Qaeda computer specialist studied electronic and nuclear engineering at Tripoli University, and was anti-Gaddafi.
He is believed to have spent time in Sudan, where bin Laden was based in the early 1990s.
After bin Laden was forced to leave Sudan, al Libi turned up in Britain in 1995 where he was granted political asylum under unclear circumstances and lived in Manchester.
He was arrested by the Metropolitan Police in 1999, but was released because of lack of evidence and later fled the UK.