A report leaked to a British newspaper appears to show that the Egyptian army participated in torture and killings during the 2011 revolution.
The report was submitted to President Mohammed Morsi earlier this year.
Egypt’s armed forces had declared their neutrality during the uprising, with the police blamed for much of the bloodshed.
Hundreds were killed and many more are unaccounted for following attempts to violently suppress the uprising.
The document leaked to the Guardian newspaper clearly implicates the armed forces in serious violations of human rights during Egypt’s 18-day revolution that led to the overthrow of Hosni Mubarak, says the BBC’s Aleem Maqbool in Cairo.
It contains testimony relating to civilians detained at military checkpoints who were never seen again.
There is also evidence presented that protesters from Tahrir Square were detained by the army and tortured inside the nearby Egyptian Museum, before being moved to military prisons.
It suggests the army delivered unidentified bodies to coroners.
The Guardian says it was leaked a chapter of a report compiled by an investigation committee which was submitted to President Morsi earlier this year but never made public.
Over recent weeks, members of the committee, which included human rights lawyers, had briefed that the military had not been co-operative during the investigation.
In 2011, the army stressed its neutrality, with the Egyptian police blamed for much of the bloodshed, our correspondent says.
But there is much more to be established about the army’s role in the initial attempt to violently suppress the revolution and in the disappearance of civilians – estimated to number anywhere between dozens and hundreds of people – who remain unaccounted for, he adds.