The US military was holding and secretly interrogating an alleged Al-Qaeda operative Monday, after covert weekend raids on Libya and Somalia which also targeted an elusive Shebab commander.

Abu Anas al-Libi was captured by special forces in Tripoli on Saturday and is now "lawfully detained by the United States military in a secure location outside of Libya," a senior US official said.

Libi, who was on the FBI's most wanted list with a $5 million bounty on his head for his alleged role in the 1998 twin bombings of US embassies in East Africa, has been taken to a US Navy warship in the region, an official told AFP.

The New York Times said he was on board the USS San Antonio, an amphibious transport currently deployed in the Mediterranean.

The Pentagon, meanwhile, revealed that US Navy SEALs had been hunting a top commander of Somalia's Islamist Shebab rebel group in a separate weekend raid on the southern Somali port of Barawe.

Abdulkadir Mohamed Abdulkadir, a Kenyan of Somali origin who fights for the Shebab under the alias "Ikrima," was the target of Saturday's strike.

His fate remains unclear, however.

Pentagon spokesman George Little said: "The operation did not result in Ikrima's capture."

Some media reports said military officials thought it was likely he had been killed, but that the elite SEALs had been forced to withdraw before they could confirm his death.

"US military personnel conducted the operation with unparalleled precision and demonstrated that the United States can put direct pressure on al-Shebab leadership at any time of our choosing," Little said in a statement.

"The United States military has unmatched capabilities and could rely on any of them to disrupt terrorist networks and plots," he warned.

The Kenyan is linked with two Al-Qaeda operatives, now deceased, who also played roles in the 1998 bombings of US embassies in Kenya and Tanzania.

State Department deputy spokeswoman Marie Harf said both operations showed only of America's global reach but also that it "doesn't forget when its citizens are killed, injured, targeted by terrorists, even sometimes when it takes a while because these are tough targets to find, that we don't forget."

She stressed however that when going after terror suspects "we have a preference, when possible to capture terrorists" partly "because of the intelligence that's gained."

The raid in Somali followed last month's siege of an upscale shopping mall in the Kenyan capital Nairobi, in which 67 people were killed.

Ikrima, identified as a top Shebab planner, was not linked to that attack but the raid was prompted by fears that he could be planning a similar assault on Western targets, the Times said.

US Secretary of State John Kerry said the capture of Libi, which triggered a furious response from Tripoli, was legal under US law, describing him as "a key Al-Qaeda figure, and he is a legal and an appropriate target for the US military."

Libi had committed "acts of terror" and had been "appropriately indicted by courts of law, by the legal process," Kerry told reporters at the Asia-Pacific Economic Cooperation summit in Indonesia.

Asked if the US had informed Libya before the raid, Kerry refused to go into specifics.

On Sunday, Libya demanded an explanation from Washington for what it called " the kidnap of one of the Libyan citizens wanted by the authorities in the United States."

"As soon as it heard the reports, the Libyan government contacted the US authorities to demand an explanation," a statement said.

Libi, 49, was indicted in the US federal court in New York for allegedly playing a key role in the east Africa bombings -- which left more than 200 dead -- and plots to attack US forces.

The arrest of Libi, whose given name is Nazih Abdul Hamed al-Raghie, paves the way for his extradition to New York to face trial, although US officials did not confirm when or if that would happen.

Citing surveillance footage, Libi's son Abdullah al-Raghie said his father had been seized by masked men armed with pistols, claiming the Libyan government was implicated, but Tripoli denied this.