Spokesman Bryan Whitman said the strike was based on "credible intelligence," and was aimed at "the principal Al-Qaeda leadership in the region." He gave no casualty figures.
Somalia's interim government says at least 30 people were killed in the attack on a southern village.
Witnesses said follow-up attacks by helicopter gunships were mounted in the region again today, though it was unclear whether these strikes were carried out by forces from the United States or Ethiopia.
The European Commission criticized the air strike, calling it counterproductive to peace efforts for the country. Somalia's President Abdullahi Yusuf says the attack was justified.
"I think [the United States was] right to strike because some of those who fled [Mogadishu] are the ones who bombed the [U.S.] Embassy in Nairobi, and also in Tanzania and a hotel in Mombasa, [Kenya]," Yusuf said. "They are wanted men and they are known terrorists. They destroyed embassies and killed people."
The raid was the first overt U.S. military action in Somalia since its unsuccessful peacekeeping mission there in the early 1990s.
One leading target is said to be Fazul Abdullah Muhammad, who is suspected of plotting the attacks on the U.S. embassies in Nairobi, Kenya, and Dar es Salaam, Tanzania, that killed 225 people. He is also suspected of attacks in neighboring Kenya in 2002 that killed 10 Kenyans and three Israelis.
Another target is said to be Abu Talha al-Sudani, identified as a Sudan-born explosives expert and the leader of Al-Qaeda's African operations.
Somali officials say the air raids came after suspected militants were seen hiding on a remote Somali island near the Kenyan border. The U.S. planes hit that island and a second site about 200 kilometers to the north.
(compiled from agency reports)