Morsi stands accused of organising a mass breakout from the Wadi al-Natrun prison during the 2011 uprising that toppled President Hosni Mubarak, as well as the murder of prison officers.
Morsi has previously said local residents freed the inmates.
Morsi and the other 130 Muslim Brotherhood members, many of them on the run, are facing the trial, along with members of Palestinian resistance movement Hamas and Lebanese group Hezbollah.
Egypt's first freely elected president was deposed by the military in a coup in July 2013 after mass protests against his rule. He is now facing four separate criminal trials on various charges.
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Meanwhile, Muslim Brotherhood leader Safwat Hegazy, also one of the defendants in the case, requested the court to respect the former president and treat him as other judges do to Hosni Mubarak in a separate trial.
Morsi's Muslim Brotherhood has been declared a terrorist organisation and authorities have punished any public showing of support for it.
"Don't compare me to any one, I am trialling the defendant Mohamed Morsi," said the Judge.
Morsi is currently in prison over charges of killing peaceful protesters, espionage, escaping from prison during the January 25 Revolution in 2011 among others.
So far he has not been sentenced in any case.