Mr Mursi was flown from Borg al-Arab prison in Alexandria for the hearing is at a police academy complex in eastern Cairo.
Only 19 of the 129 other defendants in the case, including the leader of Mr Mursi's Muslim Brotherhood group and other leading figures, are held by authorities.
The rest, including members of the Palestinian militant group Hamas and Lebanon's Hezbollah, are on the run.
Mr Mursi appeared in a separate cage from the other defendants who turned their back to the court in protest over their prosecution.
The case is rooted in the 2011 escape of more than 20,000 inmates from Egyptian prisons - including Mr Mursi and other Brotherhood members - during the early days of the 18-day uprising against ousted president Hosni Mubarak.
Authorities accuse Mr Mursi and the other defendants of plotting to "destroy the Egyptian state and its institutions", conspiring with the foreign groups who infiltrated Egypt through Gaza and using the turmoil during the uprising to organise the prison breaks.
The prosecutors said more than 800 foreign fighters entered Egypt through Gaza to take part in the storming of three prisons and killed a number of police officers and inmates.
A Brotherhood lawyer has said the trial appears aimed at "denigrating" Mr Mursi and the Brotherhood.
It is Mr Mursi's second court appearance since Egypt's popularly backed July 3 military coup. He faces three other trials on different charges, many of which carry a death sentence.
Meanwhile, gunmen on a motorbike have killed a senior Egyptian Interior Ministry official outside his home in Cairo.
The death of General Mohamed Saeed, head of the technical office of the minister of interior, suggested militants were stepping up their campaign against the state.