The Libyan government on Sunday condemned what it called the “kidnapping” of one of its citizens who was taken into custody outside his home in Tripoli in a highly unusual covert operation carried out by the U.S. military.

U.S. officials hailed the capture of Nazih Abdul-Hamed al-Ruqai, known by his alias Anas al-Libi, who was wanted in the 1998 bombings of the U.S. embassies in Tanzania and Kenya, as an intelligence coup that will disrupt efforts by al-Qaida to strengthen its franchise in North Africa. The operation, carried out by Special Forces on Saturday, represented a rare foray by the U.S. military into the controversial practice of whisking terrorism suspects out of countries with which Washington does not have an extradition treaty.

“Members of al-Qaida and other terrorist organizations literally can run, but they can’t hide,” Secretary of State John Kerry said Sunday in Indonesia, where he is attending a summit.

U.S. officials said the operation was lawful under war powers that Congress granted the executive branch after the Sept. 11, 2001, terrorism attacks. They also noted that al-Libi is on a U.N. sanctions list and has been indicted in federal court in New York.

The New York Times reported that the suspect is being interrogated aboard a Navy ship in the Mediterranean Sea.

“This operation should be a clear reminder that the United States will seek justice against those who would attack Americans and never forgets those who are victims of terrorism,” Caitlin Hayden, a spokeswoman at the National Security Council, said in a statement.

Libya’s government said in a statement issued Sunday that it had not been consulted before U.S. troops snatched al-Libi outside his home.

“Since hearing the news, the Libyan government has been in contact with American authorities and has asked them to offer clarification,” the government said, arguing that Libyans who face terrorism charges should be tried at home.

The government noted, though, that it deems its relationship with the United States a “strategic partnership” that would not be imperiled by Saturday’s operation.

Since the 2011 civil war that toppled the regime of Moammar Gadhafi, Libya has been wracked by lawlessness, growing extremism and sporadic outbreaks of violence between rival militias. The country’s newly elected government wields little authority across the oil-rich country, where militias established during the conflict continue to hold the bulk of weapons and power.

Even Libya’s military leaders, who have received counterterrorism training and funding from the United States, expressed surprise at an operation that was reminiscent of the CIA’s rendition of terrorism suspects during the years that followed the Sept. 11 attacks in 2001.

“We found out from media outlets just like everybody else,” said Aly Sheikhi, a spokesman for the Libyan armed forces chief of staff. He said he had no additional information about the incident.

The closest historical parallel U.S. officials could point to Sunday was the April 2011 detention of Amed Warsame, a Somali man who was accused of acting as a liaison between the al-Qaida branches in his native country and one in Yemen. Warsame, who was seized aboard a fishing vessel in the Gulf of Aden, pleaded guilty this spring in federal court to providing material support to terrorist organizations. Warsame was held at sea for 40 days before being arraigned in New York.

A U.S. official declined to say whether the Libyan government had been notified in advance of Saturday’s operation, but the official added that Washington considers the new government in Tripoli “a partner in the fight against al-Qaida.”

The official, who spoke on condition of anonymity to discuss a covert operation, said that al-Libi’s capture is seen as a tremendous victory because he was believed to be pivotal to the resurgence of al-Qaida’s North Africa branch. The official would not say whether al-Libi was transported out of Libya by sea or air. He also declined to say where he is being held or when he might be arraigned in federal court.

“We’re interested in what he has been doing since those times,” said the official, referring to the 1998 attack. “There are concerns that he has attempted to grow al-Qaida’s capabilities in North Africa.”

The re-emergence of Libya-based jihadists intent on striking Western targets has been a top U.S. intelligence priority since the Sept. 11, 2012, attack on American government installations in the eastern city of Benghazi.

As they celebrated al-Libi’s detention, administration officials on Sunday were largely silent on a strike by Navy SEALs on a terrorist target in Somalia that appears to have failed. U.S. Navy SEALs stormed the suspected hideout of a leader of al-Shabab, the Somali al-Qaida franchise, on Friday night, seeking to detain a senior operative of the group. The troops retreated after an intense gunfight unfolded, fearing that escalating it could result in civilian casualties, U.S. officials said.

The operation was carried out in response to last month’s brazen attack on an upscale mall in Nairobi by al-Shabab that killed dozens of people and raised concerns about the translational reach of a group that has only in recent years emerged as a global threat.

“Our personnel in the armed forces conducted two operations in order to continue to hunt down those responsible for acts of terrorism,” Kerry said. “We hope that this makes clear that the United States of America never stops in its efforts to hold accountable those who conduct acts of terror.”