The General Prosecution on Sunday referred 84 defendants on charges related to violence in the city of Qena.
The accused include the Supreme Guide of the now banned Muslim Brotherhood, Mohamed Badie, as well as high profile leaders Mohamed El-Beltagy and Safwat Hegazy.
This is the second time Badie has been referred to a military tribunal this week, after the Suez Prosecution Department referred him and 199 others to military prosecution.
The defendants face charges of sabotage, inciting violence, and storming the Qena Suez Directorate as well as a church.
Badie is a defendant in other cases related to murder, attacking public institutions in different cities after the violent dispersal of the pro-Morsi sit-ins. He has already received a number of death and life sentences.
Since the military lead ouster of Islamist president Mohamed Morsi, a severe security crackdown was launched targeting members of many Islamist movements. Protests have been dealt with a heavy response from security forces leaving tens killed, while parties and charity groups affiliated with Islamist entities were shut down.
The Muslim Brotherhood movement was declared a terrorist unit on 25 December 2013, although it was originally outlawed in September 2013. In addition, the assets of Brotherhood members and other prominent Islamists were frozen on the orders General Prosecutor Hisham Barakat. The procedure began on July 2013, immediately following the ouster of Brotherhood affiliated Morsi.