Diverging accounts of the incident emerged, with Somalia's state broadcaster reporting that a woman and two children were killed by a landmine the militants had hidden in a house in the village of El-Lahelay in Galgadud state.
The state news agency SONNA reported that the three slain militants were senior leaders of al-Qaida-linked al-Shabaab, including Olol Ali Guled, the supposed commander of the group in Galgadud.
They were killed in a "special operation" on Wednesday night, SONNA reported, without mentioning the use of a drone or the killing of the family.
The U.S. military's Africa Command, AFRICOM, which has been helping the Somali government in its yearlong offensive against al-Shabaab, confirmed three militants were killed and that AFRICOM had "medically evacuated injured civilians."
The official statement acknowledged the loss of civilian lives, but did not specifying the exact number.
"Unfortunately, civilians were injured and killed in the vicinity of the operation," AFRICOM said in a statement. "U.S. forces were not onsite for the operation and did not conduct air strikes during or in support of the operation."
A drone had tracked the militants to a house in El-Lahelay, which belonged to one of their relatives, local leader Farah Aden told Reuters by phone.
"They were seated outside the house and were busy enjoying meat and rice. As they ate the meat, the drone struck them. The house was not struck and civilians were not targeted. The civilians were hit by the shrapnel of the bomb," Aden said.
Al-Shabaab and the government communications minister did not immediately respond to Reuters requests for comment.
Last year Somalia's interior minister said the military were using Turkey's Bayraktar TB2 drones in their campaign against al-Shabaab that has pushed the jihadists out of large swathes of territory in the center of Horn of Africa country.