The commission's report accuses Thai security forces of failing to show proper care or restraint in containing a protest in southern Thailand late last year.
The report said the treatment of prisoners had violated both Thai human-rights guarantees and the International Declaration of Human Rights.
On October 25th, security forces moved to quell a protest of Thai Muslims outside a police station in the town of Tak Bai, in Narithiwat Province. The protesters were demanding the release of Muslim villagers being held without charge over allegations of giving guns to separatist insurgents.
The troops opened fire on the protesters, leaving six dead at the scene.
They then detained 12-hundred men and boys, tying their hands behind their backs before laying them in trucks for transportation to a detention center.
The report quoted a detainee as saying they had been stacked upon one another "like bricks." During the transportation, 78 more detainees died, asphyxiated or crushed to death.
The commission also found that many survivors were injured or maimed and can no longer work. It said some school-age children in the group have been forced to halt their education because of injuries and trauma.
Panitan Wattanayakorn, a political scientist at Chulalongkorn University, says the government appears to have moved to a more conciliatory approach in Southern Thailand since that incident, but separatist violence is continuing: "At least in the general sense overall it is positive, improving. But on the ground there are a lot more bombs are being exploded and people are still panicked."
The Human Rights Commission's report comes as the government's National Reconciliation Commission begins work aimed at bridging relations between the Thai Buddhist and Muslim communities. Most Thais are Buddhist, but Muslims predominate in the three southern provinces, which border Malaysia.
The Reconciliation Commission recently released its own report on the Tak Bai incident, and on the security forces' killing in April of last year of 32 insurgents holed up in a mosque.
Those reports concluded the military used excessive force in both cases, and named several senior military officers as the responsible parties.
The southern provinces have been gripped by attacks by suspected separatists since January last year. Violence is an almost daily occurrence, and more than 600 people have been killed.