A top intelligence official with Somalia's Al-Qaeda-affliated Shebab rebels was killed in a US air strike on Monday, Somalia's government said.

"In a joint operation last night by the Somali national security and the United States, Al-Shebab intelligence chief Abdishakur, also known as Tahlil, who replaced the recently arrested former chief, was eliminated," Somalia's National Security Agency said in a statement Tuesday.

"Two other Shebab members also died in the attack," it said, adding the air strike took place near the town of Saacow, 320 kilometres (200 miles) west of the capital Mogadishu and in the Middle Juba region.

In Washington, the Pentagon had announced overnight that US war planes had carried out a strike against a senior Shebab leader, but did not give the name of the person targeted.

US military spokesman Rear Admiral John Kirby said, however, that he was confident there were no "civilian or bystander casualties".

Last week Somali officials announced that Zakariya Ismail Ahmed Hersi, identified as a Shebab intelligence chief and the subject of a $3 million bounty as part of the US State Department "Rewards for Justice" programme, had given himself up to government troops and was under arrest.

He was also said to have been close to the Shebab's previous leader Ahmed Abdi Godane, who was killed by a US air strike in September. The statement from Somalia's National Security Agency said he was now in their custody.

The Shebab, however, said Zakariya had left the movement more than a year ago, before Godane's death and before Ahmad Umar Abu Ubaidah was appointed as the new leader, and that he was of little value as a source of up-to-date intelligence.

Despite the claim to have killed the head of Shebab's feared intelligence wing, known as Amniyat, who is actually in charge of the unit -- which is responsible for the group's internal security and rooting out dissidents and informers -- remains unclear.

A militant called Mahad Mohamed Ali, also known as Karate, had previously been identified by intelligence sources as Amniyat chief and had even been tipped as a potential successor to Godane.

The Shebab emerged from the Islamic Courts Union that controlled Mogadishu in 2006 before being pushed out by Ethiopian forces.

The militants were finally driven from their fixed positions in Mogadishu in 2011, and have lost several strongholds in the south and centre of the country in a recent offensive by the AU's AMISOM force.

The group, however, still controls vast rural areas from where they launch regular attacks against AMISOM troops and the country's internationally-backed government.

The United States has no permanently deployed ground force in Somalia but supports the government and sometimes deploys air power or special forces against targets linked to Al-Qaeda.