Mohamed al-Zawahiri was arrested last August, a month after Morsi's ouster by the army, and has been called to go on trial by the state prosecutor.
The military-installed authorities have since launched a crackdown against Morsi's supporters that has left more than 1,400 people dead and thousands jailed.
Zawahiri and the other suspects are accused of having set up an "Al-Qaeda-linked terrorist group" that plotted attacks against government installations, security personnel and members of Egypt's Christian minority, state news agency MENA said.
MENA did not say whether the group had actually carried out any attacks, nor did it give a date for the trial.
It said 50 of the accused were in custody, while others are on the run.
Judicial sources said investigations revealed the group had pressed members to go and fight the regime in Syria, but they were ordered to return to Egypt after June 30, 2013.
They were called back to confront Egypt's new authorities following Morsi's ouster, the sources added.
Morsi was ousted by former army chief Abdel Fattah al-Sisi after millions took to the streets on June 30 demanding his resignation.
Judicial sources said Zawahiri was being charged with having formed the group, armed its members, and trained them in manufacturing explosives and planting bombs.
They said the authorities had evidence that the group's members were trained at secret locations in the Nile Delta city of Sharqiya and in Cairo's Matareya and October 6 districts.
Since Morsi's ouster, Sharqiya has been hit by frequent militant attacks on security forces, while violent clashes in Matareya and October 6 have pitted the Islamist's backers against police.
The authorities have regularly accused Morsi's outlawed Muslim Brotherhood of financing radical Islamists linked to Al-Qaeda.
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