US forces struck two militant targets in Africa on Saturday, snatching a top Al-Qaeda suspect from the streets of Tripoli and launching a pre-dawn raid against a Shebab leader's home in Somalia.

In Libya, US forces seized a militant known as Abu Anas al-Libi, a long-sought Al-Qaeda operative indicted in the 1998 bombings of US embassies in Kenya and Tanzania.

A separate raid in the southern Somali port of Barawe failed to capture the senior militant and it was unclear whether he had been killed, but a US official said several Al-Qaeda-linked Shebab members had been slain.

It was reportedly "prompted" by the deadly militant siege on a Nairobi shopping mall last month.

The operation in Libya however appeared to be a success.

"As the result of a US counterterrorism operation, Abu Anas al-Libi is currently lawfully detained by the US military in a secure location outside of Libya," Pentagon spokesman George Little said in a statement.

A source close to Libi told AFP he was snatched by armed men in Tripoli.

Libi, who was on the FBI's most wanted list with a $5 million reward, was indicted in US federal court in New York for allegedly playing a key role in the east Africa bombings.

The attacks left more than 200 people dead.

His capture ended a 15-year manhunt for a key Al-Qaeda operative, who was born under the name Nazih Abdul Hamed Al-Raghie.

It also paved the way for Libi, 49, to be brought to the United States to face trial.

"We hope that this makes clear that the United States of America will never stop in its effort to hold those accountable who conduct acts of terror," said Secretary of State John Kerry on Sunday, speaking from the Indonesian island of Bali.

The action should also make clear that "those members of Al-Qaeda and other terrorist organizations literally can run, but they can't hide," said Kerry, speaking during a break from meetings of the Asia-Pacific Economic Cooperation forum.

The US raid took place in broad daylight with the knowledge of the Libyan government, a US official told CNN.

Libyan security services denied the claim, saying they were unaware of any kidnapping or arrest of the man.

According to the indictment, Libi and other Al-Qaeda members discussed attacking the US Embassy in Nairobi as early as 1993, and even took pictures of the mission.

In 1994 Libi allegedly drew up plans to attack the mission as well as a building that housed the United States Agency for International Development, as well as British, French and Israeli targets.

A US official said the operation in Somalia sought to capture a "high-value" Shebab leader, and that no US personnel were injured or killed.

The operation marked the most significant US assault in Somalia since commandos killed key Al-Qaeda operative Saleh Ali Saleh Nabhan in the same area four years ago.

It followed an attack by Shebab gunmen last month on the upscale Westgate shopping mall in Nairobi that left 67 people dead during a four-day siege.

"US personnel took all necessary precautions to avoid civilian casualties in this operation and disengaged after inflicting some Shebab casualties," the official said.

Declining to identify the people who died, the official said that "even in these extreme operational circumstances, the US military is very cautious to minimize civilian casualties."

Leaders of the Shebab in Barawe, one of the few ports left in the hands of the insurgents, said commandos rappelled from a helicopter but failed in their attempt to storm a house belonging to a senior commander.

The SEAL team approached and fired on the unidentified target's seaside villa by sea, according to The New York Times.

Although the Shebab leader was believed to have been killed during the assault, the SEALs had to withdraw before they could confirm the kill, a senior US official told the newspaper.

"The Barawe raid was planned a week and a half ago," a US security official told the Times.

"It was prompted by the Westgate attack."

A senior Somali government official told the newspaper that "the attack was carried out by the American forces and the Somali government was pre-informed about the attack."

Shebab spokesman Abdulaziz Abu Musab told AFP that commandos had stormed the beach by boat, but blamed Britain and Turkey.

"The bungled operation was carried out by white people, who came with two small boats from a larger ship out at sea... one Shebab guard was killed, but reinforcements soon came and the foreigners fled," he said.

"Where the foreigners had been, afterwards we saw lots of blood, so maybe we wounded some."