The militant leader was named as Moalim Aden Hashi Ayro who had trained with Al-Qaeda in Afghanistan, had been linked to the deaths of foreign aid workers, and officials said had been one of the targets of a US air strike in 2007.
There was no immediate comment from the US military on whether it was behind the attack on a house in Dhusamareb, in the Galgudud region of central Somalia.
"We are still digging debris at the house that was totally demolished. We have so far recovered 10 bodies, including that of Ayro. Three people who were injured have been taken to hospital," Abshir Moalim Ali, an elder in Dhusamareb told AFP.
A war plane dropped three large bombs on the house at about 2:00am (2300 GMT Wednesday), according to another resident, Jamal Mohamoud.
Ayro was the military leader of the Shabab group, which is on the US governments terrorist list.
Shabab spokesman Sheikh Mukhtar Robow said Ayro and another senior Islamist, Sheikh Muhyadin Omar, were among the dead from the air strike. "A US warplane bombed us in Dhusamareb district and there were casualties. This was an unprovoked attack," said Robow, whose group is a radical wing of the Islamist movement which is fighting the Somalia’s Ethiopian-backed transitional government.
Ayro and Omar are "the most important Shabab members who were victims of this foreign aggression. They passed away as they were fighting the liberation of their land," the spokesman added.
If the attack is confirmed by Washington, it would be at least the fourth of its kind that the US military has staged inside Somalia since the start of 2007.
In March last year, the Somali government said Al-Qaeda had named Aryo as its leader in the country. In his early 30s, he carried out insurgency training in Afghanistan in the 1990s and ran a secret militia training centre.
The US government added Shabab to its list of terrorist organizations in March, saying its senior leaders were believed to have trained and fought with Osama bin Laden’s network in Afghanistan.
The United States has previously given Ethiopian troops tacit support against the Islamist militia who now control of much of southern and central Somalia.
In March, the US military fired at least one cruise missile into southern Somalia near the Kenyan border, targeting an Al-Qaeda leaders and operatives believed hiding there.
In June last year, a US Navy destroyer shelled suspected Al-Qaeda targets in mountainous and remote areas in northeastern Somalia where local Islamist militants are also believed to have bases.
In January 2007, a US helicopter gunship hit insurgent positions in southern Somalia to help Somali government forces.
US officials said the previous attacks were aimed at "high-value" Al-Qaeda militants. Among them were Comoros islander Fazul Abdullah Mohammed and Kenyan Saleh Ali Saleh Nabhan and Sudanese Abu Talha al-Sudani, blamed for the 1998 bombings of US embassies in Kenya and Tanzania that killed 224 people and the 2002 bombing of a Kenyan coastal hotel that killed 15 people.
Officials said Ayro survived the January 2007 US air strike in southern Somalia but left behind blood-stained identification documents. Ayro is said to have overseen the desecration of an Italian cemetery in Mogadishu, exhuming and throwing into the sea the remains of hundreds of corpses. He reportedly ordered a makeshift mosque erected there.
In addition to leading operations against Somali and Ethiopian troops and African Union peacekeepers, Ayro has also been linked to the murders of foreign aid workers in Somalia.
Since the Islamists were ousted from Mogadishu in early 2007, they have carried out attacks against government officials, the Ethiopian forces that are backing the Somali government and African Union peacekeepers.
Western intelligence has accused Somali Islamists of having links to Al-Qaeda, which is believed to want to use war-shattered Somalia as a haven.