The capture of Nazih al-Ragye, better known as Anas al-Liby, in Tripoli by US operatives has provoked a complaint about the "kidnap" from Libya's Prime Minister Ali Zeidan.
Mr Liby is a suspect in the 1998 bombings of the US embassies in Kenya and Tanzania that killed 224 civilians.
Mr Zeidan faces a backlash from armed Islamists who have carved out a share of power since the West helped Libyan rebels oust Muammar Gaddafi two years ago.
Clearly aware of the risks to his government of complicity in the snatching of Mr Liby, Mr Zeidan said: "The Libyan government is following the news of the kidnapping of a Libyan citizen who is wanted by US authorities.
"The Libyan government has contacted US authorities to ask them to provide an explanation."
US Secretary of State John Kerry declined to say whether his government had told Libya of the raid to capture Mr Liby, whom he called a "legal and appropriate target" for the US military.
Another US official told Reuters on condition of anonymity that the Libyan government had been notified of the operation, but did not say when.
"The United States of America is going to do everything in its power that is legal and appropriate in order to enforce the law and protect our security," Mr Kerry said, when asked what perception was left when the US military snatched people off the streets of foreign countries.
He said: "He will now have an opportunity to defend himself and to be appropriately brought to justice in a court of law."
Mr Liby's whereabouts are unclear, but in similar prior cases, the US has held detainees aboard navy vessels in the Mediterranean, as well as bases in Italy and Germany.
His 19-year-old son, Abdullah al Ragye, told reporters at the family home that men had pulled up in four cars, drugged his father, dragged him from his vehicle and driven off with him.
"They had a Libyan look and Libyan accents," he said.
It was not clear if the men were linked to the Libyan state, which may either have sought to keep its distance or been sidelined by the US for fear of leaks.
When news of the snatching emerged, Mr Kerry said it proved that al-Qaeda leaders "can run but they can't hide".