The Collective Against Immunity and Stigmatisation of Communities (CISC) said the incident took place early this month in the village of Taffogo in Tougouri, citing several eyewitness accounts.
"There were many cases of kidnapping followed by summary executions," it said.
"In all, more than 40 corpses were discovered on the road between Taffogo and Bouroum," it said. "All the people had their hands tied and were blindfolded."
It said the attackers were members of the military "dressed in black clothes and hooded".
The Observatory of Human Dignity said "more than 50 unarmed civilians" were kidnapped on the road to Bouroum by soldiers.
"Nearly all the victims were Fulani, including women and children," referring to a mainly Muslim ethnic group of semi-nomadic herders spread across West Africa.
The state does not have control over more than 40 percent of Burkina's territory, according to official data.
The Observatory said government troops had "resumed the anti-terrorist fight by simply exterminating villages occupied by a certain community".
The Burkinabe army had denied repeated accusations of rights abuse, saying the perpetrators were armed groups using military materiel.