US commandos violated Libya's sovereignty when they seized the suspected ringleader of a deadly 2012 attack on the American consulate in Benghazi, the foreign ministry said on Wednesday.
Special forces carried out Sunday's stealth operation under cover of night, capturing Ahmed Abu Khatallah near Benghazi and spiriting him out of the country.
"The government condemns this regrettable infringement on Libya's sovereignty," foreign ministry spokesman Said Lassoued said in a statement, adding that Tripoli had not been informed in advance.
In announcing the operation, Pentagon spokesman Rear Admiral John Kirby would not say whether Washington gave Libya advance notice.
Also on Wednesday, Justice Minister Salah al-Marghani told a news conference that there is already an outstanding arrest warrant for Abu Khatallah.
But he said Libyan security forces had not been able to arrest him because of the security situation in the flashpoint eastern city of Benghazi.
Lassoued underlined in his statement "Libya's right to judge Abu Khattalah on its soil in conformity with its law, and asks the American government to return him to Libya."
Four Americans, including Ambassador Christopher Stevens, were killed when gunmen stormed the US consulate on September 11, 2012 and set it on fire. A CIA outpost was also targeted.
A month later Abu Khatallah told AFP he was not responsible for the attack, but admitted he had been at the consulate on the day of the attack, taking part in a demonstration to protest an anti-Islamist video that was posted on YouTube.
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The attack became a highly charged political issue in the US, raising questions about security at its missions while ex-secretary of state Hillary Clinton faced hostile questioning before lawmakers.
Republicans alleged that the White House failed to respond decisively and then tried to hide some facts in the grisly episode.
The Obama administration has accused critics of politicising a tragic event and says it has divulged all the details of the case.
US federal prosecutors have charged Abu Khatallah with murder, carrying a weapon and offering material support to "terrorism," according to an indictment.
The first charge potentially carries the death penalty.
The charges reflect accounts from Libyan officials and witnesses who have singled out Abu Khatallah as allegedly taking part in the assault that day.
The State Department had identified Abu Khatallah as a senior leader of Ansar al-Sharia, a Libyan Islamist group it brands a "terrorist" organisation responsible for a spate of attacks and assassinations.
Abu Khatallah, in his 40s, was jailed under the former regime of dictator Moamer Kadhafi in the early 1990s for his alleged involvement in Islamist organisations.
He was released in 2006 and kept a low profile until the 2011 uprising that toppled and killed Kadhafi, when he led a brigade of Islamist rebels whose members later joined Ansar al-Sharia.
The group, known as the Brigade of Abu Obeida bin al-Jarah, was suspected of assassinating rebel commander, and former Kadhafi regime official, Abdelfattah Younes.