Mexico's National Human Rights Commission (NHRC) alleges soldiers killed at least 12 people who had surrendered after a gunfight.
Raul Plascencia, who heads the government body, said evidence suggested the 12 had been killed in cold blood and not, as the soldiers say, during the gun battle.
The commission said the soldiers had tampered with the crime scene.
Eight soldiers have been detained in connection with the incident.
'In cold blood'
Twenty-two people were killed in the village of San Pedro Limon on 30 June.
The soldiers said they had come under fire from alleged gang members and the 22 had been killed in the shoot-out which ensued.
But suspicions were raised when it emerged that only one soldier had been injured in what they had described as a fierce gun battle.
Bullet marks and other evidence gathered by the NHRC suggest seven of the victims were lined up against a wall and shot "when they had been disarmed and were not resisting".
In its report, the commission says four other bodies showed marks suggesting they had been beaten with blunt objects before being killed.
Another suspect had a broken neck, apparently after someone twisted it.
Three more bodies were tampered with and the commission could therefore not establish how they had died, the report said.
The report said the crime scene had been altered in order to support the soldiers' version of events.
"Some bodies were moved and weapons were placed on all the dead bodies lying in the dirt," the report reads.
Mr Plascencia called it "one of the most serious human rights violations than can be committed".
He also called on prosecutors to investigate the alleged cover-up.
The recommendations made by the commission are not binding but the Mexican government will be required to explain publicly why it has not acted on them if it fails to comply.
Three of the eight soldiers arrested have been charged with homicide.