More politically explosive is the commission’s look at the 17 months of military rule after Mubarak’s fall, when activists protesting the generals’ conduct of the transition clashed repeated with security forces in violence that killed at least 100 protesters.

The report clearly established that security officials and the military used live ammunition against protesters during the transition and the anti-Mubarak uprising, Ragheb said.

The military repeatedly denied firing live ammunition, despite several protesters killed by bullets and pellets and despite reports by rights groups holding the army responsible.

The report established that at least one of nearly 70 missing since the uprising was tortured and died in a military prison, said Ragheb. It also details abuse by military and security officers in the days following Mubarak’s ouster, including the beating and abusing of women protesters and the conducting of ‘‘virginity tests’’ to intimidate and humiliate them.

Ragheb refused to give further specifics. The report was not made public. But he told Al-Masry Al-Youm daily thatit recommends summoning hundreds for questioning in protester killings.

Several rights activists raised concerns that findings implicating any military officials or security figures in the current Interior Ministry will be ignored.

‘‘There is every reason for Morsi and the prosecutor general he appointed to act on the findings and make sure they are translated into prompt prosecution,’’ said Hossam Bahgat, a human rights lawyer from the Egyptian Initiative for Personal Rights.

‘‘It will be a major embarrassment not to do anything,’’ he said, adding that it would also be ‘‘clear evidence’’ of what many believe to be an agreement by Morsi to grant immunity to military leaders for any alleged crimes during their rule.

Morsi appointed the latest commission at a time when his relations with the generals were rough. Just before officially transferring rule to Morsi, the military had issued a decree stripping the presidency of most of its powers.

After barely a month in office, Morsi pushed out the top generals who ruled during the transition and reclaimed his powers. His move brought no protest from the military, which many took as a sign of a backroom deal.

Gamal Eid, a lawyer who has represented protester families, pointed out that prosecutors and the court ignored a previous fact-finding mission that established evidence that could have been more incriminating.

Heba Morayef, a researcher with Human Rights Watch in Egypt, said a ‘‘protect the revolution’’ law recently issued by Morsi providing for new investigations into protester killings made no mention of the commission, meaning its findings were not binding and could be ignored.

‘‘It is a wasted opportunity,’’ she said. ‘‘Without a clear implementing mechanism, you leave room for political compromise at the expense of accountability.’’

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