The officials, who spoke on condition of anonymity because the action was carried out in secret, provided few details about the strike by an Air Force AC-130 gunship earlier this week and were uncertain whether the intended target was killed.
One official suggested that early indications showed that no high-value target was killed or captured.
At the Defense Department, spokesman Bryan Whitman declined to confirm any new strike but said in general that the United States is "going to go after al-Qaeda in the global war on terrorism wherever it takes us."
He said the nature of some military operations, especially those by special operations commando forces, requires that they be kept secret in order to preserve an advantage in future missions.
Lt. Cmdr. Marc Boyd, a spokesman at US Special Operations Command in Tampa, declined to comment.
A variety of US special operations have operated in the Horn of Africa from a base in Djibouti, a small country sandwiched between Somalia and Ethiopia.
The US Navy also has had forces in waters off the Somali coast, where they have monitored maritime traffic, boarded suspicious ships and interrogated crews in an attempt to catch anyone escaping the Somalia military operations.
Navy officials said Wednesday that no aircraft from the USS Dwight D. Eisenhower, stationed off the Somali coast, were involved in the latest strike.
Earlier this month, Ethiopian and US forces were pursuing three top al-Qaeda suspects but failed to capture or kill them in an AC-130 strike in the southern part of Somalia. A main target that time was Fazul Abdullah Mohammed, one of the three senior al-Qaeda members blamed for the 1998 bombings of the US embassies in Kenya and Tanzania.
2 killed by mortars in MogadishuThe latest operation came as Ethiopia began withdrawing troops that invaded Somalia last month to help Somalia's government drive out a radical Islamic militia that officials say has been harboring al-Qaida operatives.
In Mogadishu on Wednesday, gunmen launched several mortars at the capital's international airport, killing at least two people and wounding several others, witnesses said.
Abdilkabir Salad, who was at the gate of the airport when the mortars fell, said he saw two corpses. Another witness, Abdi Mohamed, said he saw three young men who were injured by shrapnel.
"Two mortars landed inside the airport and the other outside," said Mohamed.
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 could not enter the capital, which was ruled by the Council of Islamic Courts.