In the attacks on 25 February, the army killed 179 people in Soro village and 44 others in the nearby Nondin village, an HRW investigation found.
HRW termed the mass killings “among the worst army abuse” incidents in the country in nearly a decade.
Burkinabè authorities have not commented on the report.
Last month, public prosecutor Aly Benjamin Coulibaly appealed for witnesses to identify the group behind the mass killings. He put the preliminary death toll at 170.
Villagers who survived the attack told HRW that a military convoy with over 100 soldiers descended on Nondin village, about 30 minutes after Islamist fighters passed nearby.
The soldiers went door-to-door, ejecting residents from their homes.
“They then rounded up villagers in groups before opening fire on them,” the report added, citing witness and survivor accounts.
They arrived in Soro, about 5km (3 miles) away, an hour later, also gathering and shooting at villagers, the survivors added.
In both villages, the soldiers also shot at those who attempted to hide or escape, witnesses said.
The mass killings are believed to be retaliation by the military, which accused the villagers of aiding armed Islamist fighters.
They followed an attack by Islamist fighters on a nearby military camp in the the northern Yatenga province.
A survivor was quoted as saying that before the shootings, the soldiers accused the residents of failing to cooperate with them by not informing them of the movements of the Islamist fighters.
“The massacres in Nondin and Soro villages are just the latest mass killings of civilians by the Burkina Faso military in their counterinsurgency operations,” said Tirana Hassan, executive director of Human Rights Watch.
The Sahel country is ruled by a military junta, which seized power in a coup in 2022, promising to end the insurgency.
The violence has however continued to escalate, with more than a third of Burkina Faso controlled by jihadist groups.
International and human rights groups including the European Union and UN have accused Burkina Faso of serious human rights violations in its fight against insurgency, including the indiscriminate killings and forced disappearances of dozens of civilians.
