"The government of Burkina Faso strongly rejects and condemns such baseless accusations," communications minister Rimtalba Jean Emmanuel Ouedraogo said in a statement late on Saturday.
"The killings at Nodin and Soro led to the opening of a legal inquiry," he said.
The minister expressed his surprise that "while this inquiry is underway to establish the facts and identify the authors, HRW has been able, with boundless imagination, to identify 'the guilty' and pronounce its verdict".
HRW described the massacre as "among the worst army abuse in Burkina Faso since 2015".
"These mass killings... appear to be part of a widespread military campaign against civilians accused of collaborating with Islamist armed groups, and may amount to crimes against humanity," the New York-based group said on Thursday.
According to the Burkina statement, "The media campaign orchestrated around these accusations fully shows the unavowed intention ... to discredit our fighting forces."
"All the allegations of violations and abuses of human rights reported in the framework of the fight against terrorism are systematically subject to investigations" followed by the government and the UN high commissioner for human rights.
The junta on Thursday suspended the BBC and Voice of America radio networks from broadcasting after they aired the report accusing the army of attacks on civilians in the battle against jihadists.
The West African nation under military rule has been battered by a jihadist insurgency that swept in from neighbouring Mali in 2015.
Thousands of civilians, troops and police have been killed, two million people have fled their homes and anger within the military at the mounting toll sparked two coups in 2022.
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