Morsi, detained by the military since his ouster in July, is accused of collaborating with Palestinian group Hamas to orchestrate his escape from Wadi Al-Natroun prison in 2011 and destroying police records during the uprising.
In addition, he faces charges of espionage and of attacking police stations with the intent to kill and abduct officers and prisoners during the uprising, Al-Ahram reported.
Refaa El-Tahtawi, Morsi's chief of staff, too was remanded to detention for another 15 days pending investigation of the same charges against him. El-Tahtawi is accused of misusing his authority under Morsi to "release important information".
The Palestinian Hamas and Lebanese Hezbollah groups have been accused of aiding the plot to attack prisons, resulting in the release of inmates.
Most of the Brotherhood's top leaders are currently detained on charges of inciting violence during recent or past clashes.
Sixty-two-year-old Morsi is being held incommunicado since his ouster by the armed forces following protests on July 3.
He is also accused of "insulting judicial authority".
Throughout his one-year rule, Morsi's administration was at odds with the judiciary. The peak of the confrontation came in November 2012, when Morsi issued a constitutional declaration sacking the prosecutor-general and rendering the Islamist-led Shura Council and constituent assembly immune from judicial dissolution.
Over 1,000 people have died in a violent crackdown on Brotherhood supporters since the ouster of Morsi in the coup.
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