The Suez public prosecutors referred on Tuesday 199 people, including Muslim Brotherhood Supreme Guide Mohamed Badie, to military trial over violence which occurred in August 2013, reported state news agency MENA.
The list of defendants does not include ousted Islamist President Mohamed Mursi or Khairat al-Shater, the deputy supreme guide of the Brotherhood, reported MENA.
MENA had reported earlier on Tuesday that Mursi and Shater were among the list of defendants.
The defendants are due to appear in military court on February 23. They are facing accusations of burning military vehicles and churches in Suez in August 2013, following the dispersal of pro-Mursi sit-ins.
President Abdel Fattah al-Sisi issued on October 27, 2014 a new law which refers crimes committed against the state's public and "vital" facilities to the military judiciary.
The law was criticised by human rights organisations for expanding the jurisdiction of military tribunals on civilians.
Mursi, who is a Brotherhood politician, was outsed by Egypt's military in July 2013 following mass protests against his rule. People who supported him staged an encampment for weeks, calling for his return. On 14 August, 2013, the encampments were dispersed leaving hundreds of protesters dead.
In the aftermath of the dispersals, violence broke out in several parts of the country. In Suez, at least 30 people were killed in the violence, dozens of military personnel were injured and a military vehicle and several churches were set ablaze.
Mursi and Badie are among several leading Brotherhood figures who have been put on trial after the July ouster, facing a slew of charges. Several of them have been convicted and some have been handed death sentences.