MEXICO CITY — The federal Human Rights Commission reported on Tuesday that Mexican soldiers had executed at least 12 people, and probably 15, in late June after a supposed shootout with gang suspects, contradicting official military accounts.

The commission’s president, Raúl Plascencia, said the scene of the killings in the small town of Tlatlaya, where 22 people were reported to have died on June 30, had been altered. Bodies had been moved at the rural warehouse, he said, to suggest that everyone was killed in a shootout — the initial explanation from the Defense Department. In fact, the commission found, most of the people had surrendered before they were shot and killed.

“This is one of the worst incidents of human rights abuses ever committed,” Mr. Plascencia said.

The 93-page report, based on forensic evidence and interviews with witnesses, amounts to a bold rebuke for Mexico’s powerful military, which has become increasingly involved in fighting organized crime with aggressive tactics and little accountability.

The commission’s findings included several grisly details previously unknown or kept secret. Mr. Plascencia said one victim’s head had been twisted until his neck broke. Four other bodies showed signs of having been beaten with blunt objects before death. Bullet marks and other evidence on the warehouse’s walls suggested that seven more victims had been lined up and shot “when they were disarmed and not resisting,” Mr. Plascencia said.