Libya’s foreign ministry has said US commandos violated Libya's sovereignty when they seized the suspected ringleader of a deadly 2012 attack on the American consulate in Benghazi.
Special forces carried out Sunday's stealth operation under cover of night, capturing Ahmed Abu Khatallah near Benghazi and taking 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 the Libyan government had not been informed in advance.
In announcing the operation, Pentagon spokesman Rear Admiral John Kirby would not say whether the US gave Libya advance notice.
Libyan Justice Minister Salah al-Marghani also told a news conference that there is already an outstanding arrest warrant for Abu Khatallah.
Mr Marghani said Libyan security forces had not been able to arrest him due to the security situation in the flashpoint eastern city of Benghazi.
Mr 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 11 September 2012 and set it on fire. A CIA outpost was also targeted.
The attack shocked the and became a highly-charged political issue, raising questions about security at US missions.
Former secretary of state Hillary Clinton faced hostile questioning before lawmakers over the issue.
Republicans alleged that the White House failed to respond decisively and then tried to hide some facts in the 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.