Egypt's armed forces participated in forced disappearances, torture and killings across the country during the 2011 uprising which led to the ousting of former President Hosni Mubarak, even as military leaders publicly declared their neutrality, according to a leaked presidential report on revolution-era crimes.
The report, submitted to President Mohammed Morsi by his own hand-picked committee in January, has yet to be made public, but a chapter from it seen by the British Guardian implicates the military in a catalogue of crimes against civilians, beginning with their first deployment to the streets.
The chapter recommends that the government investigate the highest ranks of the military to determine who was responsible.
More than 1,000 people, including many prisoners, are said to have gone missing during the 18 days of the revolt. Scores turned up in Egypt's morgues, shot or bearing signs of torture, according to the Guardian.
Many have simply disappeared, leaving behind desperate families who hope, at best, that their loved ones are serving prison sentences that the government does not acknowledge.
The findings of the high-level investigation, implicating Egypt's powerful military, will put pressure on Morsi, who assumed power from the Supreme Council of the Armed Forces after his election in June and has declined to prosecute any officers, despite allegations that some participated in abuse.
They could also figure in the retrial of Mubarak and his former interior minister Habib al-Adly, who are set to return to court on Saturday to face charges – perhaps supported by new evidence from the report – that they were responsible for killing protesters during the revolt.
Mubarak and Adly were sentenced to life in prison for failing to prevent the deaths of over 800 protesters during the 18-day uprising that began on January 25, 2011.
The rulings sparked nationwide outrage, with thousands taking to the streets to vent their anger that no one had been found directly guilty of killing the protesters.
Among the incidents explored in the chapter, which focuses on the fate of those who went missing or were forcibly disappeared, investigators found that members of the armed forces detained an unknown but probably large number of civilians at a checkpoint on a road south of Cairo who have not been seen again; detained and tortured protesters in the Egyptian Museum before moving them to military prisons, killing at least one person, and delivered to government coroners in the capital at least 11 unidentified bodies, believed to be former prisoners, who were buried in paupers' graves four months later.
"The committee found that a number of citizens died during their detention by the armed forces and that they were buried in indigent graves, as they were considered unidentified," the report says, according to the Guardian, adding that authorities did not investigate, despite evidence of injuries and severe torture.
"The committee recommends investigating the leaders of the armed forces about the issuance of orders and instructions to subordinates who committed acts of torture and enforced disappearance," it states.
The military declined to comment on the report, saying it could take up to three weeks to respond. A source at the president's office told the Guardian that Morsi had not seen the findings, which were being investigated by the prosecutor general.
"As soon as results appear, they will be made public," the source said. "The findings you mentioned are speculative, and not authentic. We haven't received the findings from the committee, and the investigations are still ongoing."
Protesters and opposition politicians have long called for the military to be held accountable for scores of alleged incidents of torture and killings during the uprising and 16 months of military rule that followed. The military has prosecuted at least four people, including three low-level conscripts, for incidents that occurred later in 2011, but no member of the armed forces is known to have faced charges for abuse or killings during the revolution.
The 16-member fact-finding committee, appointed by Morsi last July, investigated 19 violent incidents and submitted a roughly 800-page report to Morsi and the prosecutor general, Talaat Abdallah, but neither has released or publicly responded to the report's findings and recommendations, noted the Guardian.