Abdirahman Dinari, a Somalia government spokesman, confirmed the offensive on Tuesday.
A US official, who spoke on condition of anonymity, said at least one AC-130 gunship was used in the attack.
Dinari told AFP: "We know that a US gunship raided targets of al-Qaeda in southern Somalia sometime yesterday afternoon.
"The target was a small village called Badel where the terrorists were hiding. And the gunship did hit on the exact target."
Güncelleme Tarihi: 20 Eylül 2018, 18:16
Dinari said there were casualities from the raids.
"Absolutely a lot of people were killed. So many dead people were lying in the area, but we do not know who is who, but the raid was a success," Dinari said.
CBS television network said the targets included the senior al-Qaada leader in East Africa and an al-Qaeda operative wanted for his involvement in the 1998 bombings of the American embassies in Kenya and Tanzania.
Air Force AC-130 gunships are heavily armed aircraft with elaborate sensors that can go after discreet targets - day or night. They are operated by the special operations command and have been used heavily against the Taliban in Afghanistan
US navy vessels have been deployed off the coast of Somalia to make sure al-Qaeda or allied activists do not escape the country, the US state department has said.
US officials said after the September 11, 2001, attacks that extremists with ties to al-Qaeda operated a training camp at Ras Kamboni in Somalia and that al-Qaeda members are believed to have visited it.
The alleged mastermind of the 1998 US embassy bombings in East Africa, Fazul Abdullah Mohammed, escaped to Ras Kamboni, according to testimony from one of the convicted bombers.
The 1998 bombings of the US embassies in Kenya and Tanzania killed more than 250 people. The 2002 attack on an Israeli-owned hotel in Kenya killed 15.