Somali forces supported by US troops shot dead 10 Somalis, including three children, in a village near Mogadishu, a witness and local officials told Reuters.
The involvement of US troops was confirmed by US Africa Command, which said it was investigating reports of civilian casualties.
The Somali army initially said no civilians were killed and all the dead were members of the al Qaeda-linked al Shabaab militia fighting to overthrow the UN-backed government and impose strict Islamic law.
It later issued a second statement saying some civilian casualties were reported.
“We also understand there are civilian casualties which the Federal Government is investigating to find out the truth about this. We urge Somali people to co-operate fully with government on this matter,” the Somali army said.
The incident is likely to provoke questions in Washington about the growing US footprint in the Horn of Africa nation, which has been torn apart by civil war since 1991. A US Navy Seal was killed in Somalia in May, the first US combat death there since 1993.
The White House has granted the US military broader authority to carry out strikes in Somalia against al Shabaab, in the latest sign President Donald Trump is increasing US military engagement in the region.
Local elders said the keenness to engage left the US open to being unwittingly drawn into clan feuds, stoking tensions between Somalis and the United States.
The village attacked, Bariire in Lower Shabelle, about 50 km from the capital, is at the centre of a feud between two powerful and well-armed clans, lawmaker Dahir Amin Jesow said.
He said those killed were farmers who had armed themselves to defend themselves against the rival group.
“The two clans who fought misinformed the US forces,” he said, adding one group may have tipped off security forces the other side were insurgents.
Witness Warsame Wador told Reuters the dead were farmers who were asleep when the raid began just before sunrise.
“It was this morning when white and Somali forces entered the farm. All 10 people were asleep and I ran for my life,” he said. “As I ran away I could see four armoured vehicles outside.”
Reuters viewed nine bodies at Madina hospital. An injured man later died, medical staff said. The dead children were eight, nine and 10 years old, said clan elder Abukar Osman Sheikh.
“They were sleeping in their farm when US and Somali forces came onto their farm and opened fire. Last year, the US killed my people in Galkayo in a deliberate strike. We shall not bury them. We shall no longer tolerate it,” he said.
A September 2016 air strike in Galkayo killed at least 10 pro-government fighters, the US acknowledged.
Madina hospital was packed with people who said they were relatives of the dead. Insurgents do not typically accompany their dead to hospitals in the capital, controlled by government.
“These dead bodies were innocent farmers,” Ali Nur, deputy governor of lower Shabelle region, told Reuters.
But the Somali National Army (SNA) issued a statement saying eight insurgents were killed in an operation carried out with “international partners”.
“The SNA carried out an operation this morning against a farm in Bariire with known al-Shabaab presence,” the statement quoted General Sheegow, commander of the 20th Brigade, as saying.
“Al Shabaab started shooting at SNA forces after our soldiers entered the farm. The individuals shooting at the SNA were al Shabaab fighters, they were not farmers.”