"The relevant departments have been asked to determine the authenticity and origin of this video, as well as the identities of the individuals concerned, so that they can be held accountable for their actions, if the facts are proven," the general staff said in a statement.
Nothing in the video serves to identify the location, the date or the individuals involved, some of whom are dressed in military uniforms.
In July, the Burkinabe army condemned acts of corpse mutilation by people suspected of being soldiers and civilian auxiliaries seen in videos widely shared on social media.
Fellow junta-led Mali's armed forces likewise distanced itself from a video showing similar acts by men in army uniforms and with military insignia.
"This unspeakable act is contrary to the military and moral values inculcated in armed forces personnel.... and transgresses the rules of engagement for units in the field," the general staff said on Sunday.
"All operations to reconquer the national territory are conducted with the greatest respect for human rights," it added.
Rights groups have frequently accused the Burkinabe army of carrying out extrajudicial executions, which it has always denied, sometimes blaming armed groups using military equipment.
In April, Human Rights Watch accused the army of executing at least 223 civilians, including 56 children, at the end of February in the north of the troubled country.
Frequently the target of jihadist attacks, Burkina Faso has been led by a military junta that led a coup d'etat pledging to clamp down on armed militant groups.
Since 2015, violence attributed to armed movements affiliated with al-Qaeda and the Islamic State group has claimed more than 26,000 lives, including more than 13,500 since the September 2022 coup.
More than two million people have also been forced to flee their homes inside the country.
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