The three judges who had presided over the trial of Mohamed Badie and 34 co-defendants, including his two deputies, recused themselves on October 29 for what they said were "reasons of conscience".
Badie and his two deputies, Khairat al-Shater and Rashad al-Bayoumi, face charges of inciting the murders of nine protesters who stormed the Brotherhood's Cairo headquarters on June 30.
If found guilty, they could face the death penalty.
Three other accused leaders of Brotherhood also face murder charges while 29 are charged with participating in acts of violence.
Morsi, Egypt's first democratically elected president, was ousted by the army on July 3.
His supporters deny allegations of Morsi’s opponents and point to the Muslim Brotherhood's victories in elections held after Mubarak's overthrow.
Morsi himself was put on trial on November 4.
Badie also faces another trial starting on December 9 on new so-called "incitement to murder" charges.
The trials are part of a massive crackdown on the Brotherhood by the military-installed authorities since July 3.
More than 1,000 people have been killed since Morsi's ouster -- mainly his supporters -- and the authorities have arrested some 2,000 Islamists, including most of the Brotherhood's leadership.
NJF/NJF