Libya's government has summoned US ambassador Deborah Jones to seek clarification over the capture of senior al-Qaeda suspect Nazih Abdul-Hamed al-Ruqai, known by his alias Abu Anas al-Liby, from the capital, Tripoli.
"Justice Minister Salah al-Marghani summoned the ambassador of the US on Monday morning to ask for answers to several questions relating to the case" of Abu Anas al-Liby, a ministry statement said on Tuesday.
Liby, who was snatched by the US special forces in Tripoli on Saturday, is wanted by the US in connection to the bombing of American embassies in Uganda and Kenya in 1998 that left 224 people dead.
His wife, Uma Abderahman, told Al Jazeera that her husband was taken from his home by masked men.
"There were at least ten of them and they were all armed, with silenced weapons," she said. "It seems like they had drugged him."
In a statement of its own, Human Rights Watch called on the US to ensure al-Liby was quickly charged before a judge and given access to a lawyer in accordance with international law, adding that he should be tried in a civilian court.
A US interrogation team is questioning the alleged senior al-Qaeda figure who was whisked onto a navy ship in the Mediterranean Sea, US officials said.
The Libyan Prime Minister, Ali Zeidan insisted on Tuesday that all Libyans should be tried on home soil, and the country's highest political authority called the raid a violation of Libya's sovereignty.
Zeidan added that the US raid would not hurt Libya's relations with Washington.
"Our relationship with the USA is important, and we care about that, but we care too about our citizens, which is our duty," Zeidan said at a press conference with his Moroccan counterpart Abdelilah Benkirane during a three-day visit to Rabat.
"They helped us with our revolution. Our relationship will not be affected by this event, which we will settle in the way that we need to."
Liby's capture has provoked a complaint about the "kidnap" from the Western-backed government. US officials declined to say if the Libyan government was given advance notice.
US Secretary of State John Kerry on Monday defended the capture, saying complaints about the operation from Libya and others are unfounded.
Kerry said the suspect was a “legal and appropriate target” for the US military and will face justice in a court of law.
The raid has angered powerful armed groups in Libya, who say the US violated Libyan sovereignty and accuse the Libyan government of colluding with the raid - or at least turning a blind eye.
Many armed groups have posted messages on social networking sites calling for revenge attacks on strategic targets including gas export pipelines, planes and ships, as well as for the kidnappings of Americans in the capital.
The US will move about 200 Marines to a US base at Sigonella, Italy from one in Spain in the next day or so, US military officials said, bolstering the US ability to respond to any fallout from the raid in Libya.