At least 10 civilians, including three children, have been killed in a joint raid by Somali forces and US troops in the country's south, local officials said.

The attack, which took place in the early hours of Friday, targeted a farm on the outskirts of the town of Bariire in the southern Lower Shabelle region.

"These local farmers were attacked by foreign troops while looking after their crops," regional Deputy Governor Ali Nur Mohamed told reporters in the capital Mogadishu.

"The troops could have arrested them because they were unarmed, but instead shot them one by one mercilessly."

Three children, aged eight to 10, and a woman were among the dead, Mohamed said. Their blanket-wrapped bodies were laid out in a grassy courtyard for display.

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The Somali army initially said no civilians were killed and all the dead were members of the al-Qaeda-linked al-Shabab militia, which is fighting to overthrow the UN-backed government and impose strict Islamic law.

It later issued a second statement saying some civilian casualties had been reported.

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.

African Union forces and Somali soldiers recaptured Bariire, located 40km southwest of Mogadishu, from the armed group al-Shabab six days ago.

The involvement of American troops during Friday's attack was confirmed by US Africa Command, which offered no further details.

"The Somalia National Army was conducting an operation in the area with US forces in a supporting role," a spokeswoman for US Africa Command told Reuters news agency.

A statement by the US military said it is aware of the "civilian casualty allegations" and is conducting an assessment into the situation.

Bariire is at the centre of a feud between two powerful and well-armed clans, legislator Dahir Amin Jesow said. He said those killed were farmers who had armed themselves to defend against the rival group.

"The two clans who fought misinformed the US forces," said Amin, adding one group may have tipped off security forces that the other side were rebels.

Witness Warsame Wador told Reuters the dead were farmers who had been asleep when the raid began just before sunrise.

"It was this morning when white and Somali forces entered the farm. All the 10 people were asleep and I ran for my life," he said. "As I ran away, I could see four armoured vehicles parked 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 into 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.

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Al-Shabab, which has become the deadliest armed group in Africa, continues to hold vast areas of rural Somalia after being chased out of major cities in recent years by the multinational African Union force and Somali troops.

The group continues to threaten the fragile central government and carry out deadly attacks in neighbouring countries, notably Kenya.

Earlier this year, President Donald Trump approved expanded military operations against al-Shabab, including more aggressive air raids.

The United States and Somalia in recent weeks said attacks have killed al-Shabab leaders responsible for planning and executing deadly attacks in Mogadishu, where high-profile areas such as hotels and military checkpoints are often targeted with deadly bombings.