US Africa Command - the American combat command for the African continent - said on Friday that US forces had been working "in a supporting role" with the Somali army near the capital Mogadishu when ten people were killed.
"We take any allegations of civilian casualties seriously, and per standard, we are conducting an assessment into the situation to determine the facts on the ground," it added in a statement.
Local officials said ten civilians were shot dead in Friday's attack at a farm on the outskirts of the town of Bariire in the southern Lower Shabelle region. Three children were among those killed.
Read more: Tackling the security crisis in Somalia
Initially the Somali army denied that civilians had been among the dead, insisting they were members of the al Qaeda-linked al Shabaab militia that seeks to impose strict Islamic law on the east African country. It later admitted that civilian casualties had been reported.
Journalist Khader Mohamud Hared tweeted the two conflicted statements from Somalia's ministry of information.
A Somali commander said Al Shabab militants started shooting at its forces when soldiers entered the farm, insisting that their targets were not farmers.
African Union forces and soldiers recaptured Bariire, 40 kilometers (25 miles) southwest of the capital, Mogadishu, from the Islamist group just six days ago.
Local leaders 'not informed'
Two local officials accused the US troops of involvement in the deaths with one saying the raid was carried out without their knowledge.
Read more: US and Somali forces strikes Al-Shabab command post
"We are still confused on why the US troops did this terrible act in which they have killed at least 10 farmers," Ali Nor Mohamed, the region's deputy governor told the German news agency dpa.
Parliamentarian Mahad Salad took to Facebook to confirm the attack "at the hands of US troops," but later removed the post.
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The Reuters news agency cited local elders as saying that instead of hitting Al Shabaab rebels, the US troops may have unwittingly been drawn into local clan feuds. Lawmaker Dahir Amin Jesow said those killed were farmers who had armed themselves to defend themselves against a rival group.
Trump's new offensive
America's military presence in Somalia was bolstered in March by US President Donald Trump's order, granting new powers to intervene against al Shabab in the Horn of Africa. But their involvement in the operation to weaken the Islamist group has not been without controversy.
Last September, a US airstrike on the Islamist militia in northern Somalia left a dozen Somali troops dead, leading local residents to burn American flags and posters of then US President Barack Obama in protest. Again, the US military was accused of being tricked into making the air raid against a rival of a Somali faction.
mm/kl (dpa, Reuters)