"I am particularly concerned that a journalist was expelled following the reporting on a video that appears to show extrajudicial executions of children in the northern town of Ouahigouya," said Volker Turk, the United Nations' high commissioner for human rights.
"When such grave allegations come to light, it is the duty of the authorities to promptly hold thorough, impartial and transparent investigations to establish the facts and, if applicable, ensure that those responsible are brought to justice."
Burkina Faso recently expelled correspondents from the Liberation and Le Monde newspapers, in the latest move against French media by the ruling junta.
"Protection of independent voices is more necessary than ever - to enable scrutiny, to facilitate accountability, and to allow the space for the Burkinabe people to build a resilient, stable and inclusive society together," said Turk.
Since military leader Ibrahim Traore seized power in September, the activities of all political parties and civil society organizations in Burkina Faso have been suspended.
Media freedoms have been curbed, with the authorities suspending Radio France Internationale and France 24 broadcasts.
Both RFI and France 24, which cover African affairs closely and are popular in French-speaking west African nations, have also been suspended in Mali.