Morsi, who was ousted on July 3 after massive countrywide protests against his rule, and 14 other top leaders of Muslim Brotherhood are facing charges of murder and violence at the Ittihadiya presidential palace clashes in December 2012.
At least 10 people died in the clashes which broke out after pro-Morsi protesters attacked a sit-in held by opponents of a presidential decree which had granted the Islamist leader expanded powers.
If found guilty, Morsi and 14 others could face lifetime imprisonment or the death penalty.
A military helicopter flew 62-year-old Morsi from a secret detention centre to the court at the Police Academy on the eastern outskirts of Cairo. Other defendants were transferred to court via armoured vehicles from Tora prison.
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Security forces are on high alert after supporters of the former president called for major protests.
The heavily-fortified trial venue has already been transformed into a courthouse for the trial of another former president, Hosni Mubarak, who was toppled in a 2011 uprising.
The National Alliance to Support Legitimacy, a pro-Morsi coalition backed by the Muslim Brotherhood, described the trial as a "farce", decrying what they call "illegal" measures against the country's first freely elected president.
Morsi supporters accuse the army of staging a 'coup' against the elected president and reversing the democratic gains of the 2011 uprising that toppled Mubarak.
The military, however, says it was merely responding to the peoples' will after millions took to the streets to protest Morsi's one-year divisive rule.
The Ministry of Interior said it will stand against any assaults, abiding by "legal procedures regulating the use of firearms". It added the ministry is "accurately monitoring" the activities of the Muslim Brotherhood.