State news agency Mena said the mooted charges against Morsi included conspiring with the Palestinian Islamist group Hamas, killing prisoners and officers "deliberately with prior intent", kidnapping officers and soldiers, and setting fire to the prison of Wadi el-Natroun.
They relate to his escape from the prison in 2011, when he was arrested during the uprising against Mubarak, and provide legal grounds for his continued detention.
Morsi has been held by the military since the army ousted him from office on July 3 following huge street protests against his troubled, one-year rule. Washington has previously called for him to be freed.
His Muslim Brotherhood denounced news of the accusations.
"At the end of the day we know all of these charges are nothing more than the fantasy of a few army generals and a military dictatorship," Brotherhood spokesman Gehad El-Haddad said. "We are continuing our protests on the streets."
Throwing down the gauntlet to the Brotherhood, army chief General Abdel Fattah al-Sisi has called on Egyptians to rally nationwide on Friday to give the military a "mandate" to confront weeks of violence unleashed by Morsi's removal.
A military official said the army had given Morsi's Muslim Brotherhood a Saturday deadline to end its resistance and join a military-set road map to new elections, signalling a turning point in the confrontation.
The Brotherhood fears a crackdown to wipe out an Islamist movement that emerged from decades in the shadows to win every election since Mubarak's fall but then struggled to tackle Egypt's growing economic and social woes.There may be a civil war there by the time Shabbat ends. Shabbat Shalom everyone.