The country's biggest trial since the army removed Morsi last July after a turbulent single year in office was adjourned until Monday.
About 500 defendants faced charges at a court in Minya, south of Cairo, with the trial of the remainder due to begin on Tuesday, state news agency MENA reported.
The legal proceedings are part of a crackdown by the military-installed authorities on Morsi's Islamist supporters who remain steadfast in demanding his reinstatement.
The defendants are accused of attacking both people and public property in southern Egypt in August, after security forces broke up two Cairo protest camps set up by Morsi supporters.
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They are also charged with committing acts of violence that led to the deaths of two policemen in Minya, judicial sources said.
Monday's session is set to further examine charges against those defendants who attended today's hearing.
The court session was closed to the media, so it was unclear how many of the accused appeared in person.
Among the defendants are the supreme guide of the now-banned Muslim Brotherhood, Mohammed Badie, and several other leaders of the movement, MENA reported.
Hundreds of people died in the August 14 assault on the two Cairo protest camps and in subsequent clashes that day.
Amnesty International says at least 1,400 people have been killed in violence across Egypt since then, while thousands more have been arrested.
Morsi is himself currently on trial in three different cases, including one for inciting the killing of protesters outside a presidential palace during his presidency.