A report by Amnesty International has accused US African Command troops of killing innocent Somalia farmers at Lower Shebelle region in March this year.
The US Africa Command is responsible for training African troops in Somalia, who are attached to the AMISOM forces.
In the statement released on Tuesday, Amnesty International accused forces of targeting innocent civilians instead of Al-Shabaab militants.
"It's bad enough that the US Africa Command appears not to know who its air strikes are actually killing and maiming in its secretive war in Somalia," Abdullahi Hassan, a Somalia researcher for Amnesty, said in a statement.
"But it's reprehensible that Africom offers no way for those affected to contact it and has failed to reach out to the families of victims after its version of events was called into question in this case."
Amnesty says it interviewed 11 people about the March 18 strike, including co-workers and family of the men killed when their car was hit in Lower Shabelle, a hotbed of the Islamist insurgency in southern Somalia.
It said all those interviewed in the investigation "were adamant that none of the men was a member of Al-Shabaab".
Africom spokesman John Manley told AFP that "as explained to Amnesty International, based on detailed methods and a body of multi-intelligence reporting, to include the actions observed from the vehicle, US Africa Command arrived at reasonable certainty the vehicle and its occupants were al-Shabaab and actively supporting al-Shabaab operational activity."
"US Africa Command minimises the risk to civilians by following a thorough, reasonable methodology that accounts for weapons effects and mitigates risk to civilians."
The statement comes barely 24 hours after Al-Shabaab militants attacked a US training center in Ballidogle military airbase which is one of most guarded areas.
Military sources said the US Africa Command troops and the special forces attached to Somali National Army managed to kill all militants who stormed the base.
In August, Somalia government also accused Kenya Defense Forces of destroying infrastructure for communication on the pretext of war against Al-Shabaab.