The official, who spoke on the condition of anonymity, said the strike was likely carried out against targets in the southern part of the country.
A similar airstrike conducted by U.S. Special Operations forces Jan. 7 was believed to have killed eight to 10 people, but U.S. officials willing to speak about the attack said they did not believe the intended targets — Al Qaeda operatives wanted in connection with the 1998 U.S. Embassy bombings in nearby Kenya and Tanzania — had been hit.
Pentagon spokesman Bryan Whitman would not confirm Wednesday whether another airstrike had been conducted but did say the U.S. would continue to monitor and attack Al Qaeda targets in Somalia.
"We have for some time been concerned about Al Qaeda operating in that region and that's why we're working with countries throughout that area of responsibility to identify, track, seek, capture and if necessary kill Al Qaeda working, taking safe haven, operating in that region," he told reporters.
When asked about a second U.S. gunship attack in Somalia, another U.S. defense official said "there are known terrorists who are seeking to try to take harbor, to plan and conduct operations in that region." The official spoke on the condition of anonymity because of the nature of the information.
Meanwhile, gunmen launched several mortars at Mogadishu International Airport on Wednesday, wounding at least three civilians, witnesses said.
Abdi Mohamed, who was nearby, said he saw three injured young men who were hit with shrapnel.
"Two mortars landed inside the airport and the other outside," said Mohamed. "There were three planes on the runway when the attack happened."
The runway was not damaged, said the director of the airport.
The attack comes one day after Ethiopian troops began withdrawing. The intervention of Ethiopia last month prompted a military advance that was a stunning turnaround for Somalia's two-year-old government. Without Ethiopia's tanks and fighter jets, the administration could barely assert control outside one town and couldn't enter the capital, which was ruled by the Council of Islamic Courts.
On Tuesday, Somali government spokesman Abdirahman Dinari said Ethiopia helped chase the Islamic movement from the capital and much of southern Somalia, but that it was time for the neighboring forces to leave. It was unclear when the Ethiopian withdrawal would be completed.
"As of today, the Ethiopian troops have started to withdraw from Somalia. We are grateful that they played an important role in the restoration of law and order in the country," Dinari said.
But the potential for violence in this chaotic Horn of Africa nation remains great because of clan rivalries, resentment of the government's Ethiopian backers and a threat of guerrilla war from remnants of the Islamic movement.
Many Somalis were angered by the presence of Ethiopian forces; Somalia, a Muslim country, and Ethiopia, which has a large Christian population, fought a brutal war in 1977.
Nearly 200 people gathered at the former National University in Mogadishu, cheering as the Ethiopians moved out on trucks and tanks. "Leave us alone and let us solve our problems," the crowd chanted.
"I am very happy the Ethiopians are leaving because it will end clashes in which civilians are the victims," said Ilmi Shardi Mahad, a resident of Mogadishu's Hurwa district, considered a hotbed of support for the Islamic movement.
Ethiopian Prime Minister Meles Zenawi said Wednesday that "quite a few" Somali fighters captured by his forces were being held in Ethiopia. He declined to elaborate.
A Somali government soldier said Wednesday that he saw a wounded Islamic movement official this week being held by Ethiopians in the Somalia city of Kismayo. He said the wounded man was Sheik Ahmed Madobe, governor of the Islamic courts in Kismayo.
"He had injures in one of his legs," said government soldier Deq Ibrahim.
The Ethiopian withdrawal raises a sense of urgency for a proposed African peacekeeping force to arrive quickly.
The African Union Peace and Security Council has approved a plan to send about 8,000 African peacekeepers, including nine infantry battalions, to Somalia for a six-month mission that would eventually be taken over by the U.N. Malawi and Uganda have said they want to contribute troops, but no firm plans are in place.
The Associated Press along with FOX News' Nick Simeone and Mike Emanuel contributed to this report.