The 85-year-old longtime autocrat's previous conviction for failing to stop the killings was overturned on appeals earlier this year, leaving still open questions about who ordered the use of deadly force against protesters and who carried out those orders.
The naming of former prison and top intelligence officials in the case appeared to intertwine Mubarak's trial with accusations facing his successor, Mohammed Morsi, who was ousted in a popularly-backed coup July 3 just one year after his election.
Morsi has been held since at an undisclosed military facility and is being investigated on allegations that he and other Muslim Brotherhood leaders conspired with the Palestinian Hamas group in the neighbouring Gaza Strip to escape from prison during the anti-Mubarak uprising.
That allegation was raised again in court today by defence lawyers who suggested that Hamas militants were behind the attacks on prisons and police stations in the northern Sinai Peninsula, which borders Gaza.
As the trial resumed, the army continued its largest offensive in years against militants in northern Sinai.
Security officials said today they uncovered explosives aimed at an Egyptian border post near a tunnel from Gaza, with a detonating wire leading back through a tunnel to Gaza.
Military intelligence officials said the discovery was another sign that Gaza-based militants are involved in attacks on Egyptian security forces. The officials spoke on condition of anonymity because they were not authorised to speak to the media.
Over the past weeks, the military has bulldozed homes along the Gaza border and caved in tunnels beneath them in preparations for creating a buffer zone to reduce weapon smuggling and militant crossings.
Brotherhood and Hamas officials have long denied any connection to the prison breaks or attacks on security forces in Sinai. The Brotherhood says the allegations are part of a propaganda blitz that has portrayed the group as a terrorist organisation that must be banned.
"The authority of power and of the coup turned the victims into the perpetrators and the perpetrators into the victims... completely and clearly surpassing the simplest rules of justice, which are essential to the viability and stability of nations," the Brotherhood said in a statement today.
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