Mohammed Fahmy al-Qarmuty the egyptian Judge said, he and his colleagues were retiring from the case for “reasons of conscience”.
The move comes days before the test of the previous leader, Mohammed Morsi.
He is to stand test on 4 November, on allegations of inciting killing and violence in attachment with clashes out-of-doors the presidential castle in December 2012.
Khairat al-Shatir and Badie, were apprehended in the days following Mr Morsi’s overthrow on 3 July.
Mr Badie was a prominent number at the Brotherhood’s dispute bivouacs in Cairo, but went into hiding as the military-backed interim government increased its efforts to shut down the disputes. He was apprehended in August.
Mr Morsi is also in a trial on charges of killing and violence in attachment with deadly clashes out-of-doors the presidential castle in December 2012.
His supporters broadcast on Monday that the previous leader had rejected the administration of the court where the trial is due to take place.