The report, which included comments from unnamed local sources in Somalia, said USA troops using faulty intelligence fired on unarmed civilians.
The US military did not kill any civilians when it accompanied Somali forces on a deadly raid in August, US Africa command said.
Details have emerged that suggest that the US forces carried out the operation - meant to retake and hold Bariire from the al Qaeda-affiliated al-Shabaab - without sufficiently vetting information and using untrustworthy intelligence, according to the Daily Beast.
Citing unnamed sources, The Daily Beast said U.S. Navy Seals fired on unarmed farmers in the village and then took pictures of those shot with weapons falsely planted beside their bodies to appear as though they were armed.
"After a thorough assessment of the Somali National Army-led operation near Bariire, Somalia, on August 25, 2017 and the associated allegations of civilian casualties, US Special Operations Command Africa has concluded that the only casualties were those of armed enemy combatants", AFRICOM said in a statement.
Africom said in the statement it was "aware of the civilian casualty allegations" and that it was "conducting an assessment into the situation to determine the facts on the ground".
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"Before conducting operations with partner forces, SOCAF conducts detailed planning and coordination to reduce the likelihood of civilian casualties and to ensure compliance with the Law of Armed Conflict", the statement said. A separate statement Wednesday by the U.S. Africa Command says there are now more than 500 U.S. military personnel in the Horn of Africa nation.
Somalia has been riven by civil war since 1991.
In addition, the outlet reported that the information was buried after the US government put pressure on Somali officials.
AFRICOM's statement did not address The Daily Beast story.
Local elders called a news conference in the capital Mogadishu and displayed nine bodies, two of them children, saying they were civilians killed in cold blood by Somali troops.
Trump this year granted a request from Africom to give commanders more authority to conduct airstrikes and raids against al-Shabaab without high-level, interagency reviews.
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