The ousted president is to be questioned for an initial 15-day period, a judiciary order said.
Mohamed Morsi has been held at an undisclosed location since his removal by the military on July 3.
The announcement comes as supporters and opponents of the deposed president prepare to stage mass rallies in Cairo.
The order issued on Friday is the first official statement on Mohamed Morsi’s judicial status since he was overthrown.
It says the former president is suspected of conspiring with Hamas, which rules the Gaza Strip and has strong links with Mohamed Morsi’s Muslim Brotherhood, during the uprising against former President Hosni Mubarak.
The state-run Mena news agency says Mohamed Morsi is accused of colluding with the Palestinian group to storm police stations and jails, “setting fire to one prison and enabling inmates to flee, including himself, as well as premeditated killing of officers, soldiers and prisoners”.
Mohamed Morsi and several Muslim Brotherhood leaders were freed during a breakout at a Cairo prison in January 2011.
A spokesman for the Muslim Brotherhood, Gehad el-Haddad, described the accusations as “ridiculous”. He told Reuters news agency that the order marked the return of the “old regime”.
The army has warned any attempt to use violence during mass rallies planned on Friday will be “dealt with decisively and with force”.
On Wednesday, army chief General Abdel Fattah al-Sisi called on people to take to the streets to give the military a mandate to confront violence and “terrorism”.
Since Mohamed Morsi was ousted, dozens of people have died in clashes between supporters and opponents of the Islamist leader.
Militants have also staged deadly attacks in the Sinai peninsula.
The Tamarod movement that organized protests which preceded Mohamed Morsi’s removal has urged its supporters to take part in Friday’s rallies.
“We call on all of the great Egyptian people to gather in the squares on Friday to officially demand that Mohamed Morsi be put on trial and to support the Egyptian armed forces in its coming war on terrorism,” it said.
Some analysts say the military could be preparing to move against sit-ins by Morsi supporters, including one in front of the Rabaa al-Adawiya mosque in a Cairo suburb.
Mohamed Morsi narrowly won the presidential election in June 2012 to become Egypt’s first democratically elected president, but his opponents accused him of trying to impose an Islamist agenda on the country.
Interim President Adly Mansour has set out a “roadmap” towards a revision of the constitution introduced by Mohamed Morsi and for fresh elections in early 2014, but this has been rejected by the Muslim Brotherhood.
Hisham Qandil, who was prime minister under Mohamed Morsi proposed his own roadmap on Thursday, involving:
There has been no official response to Hisham Qandil’s suggestions, and military spokesmen have previously given the Muslim Brotherhood a deadline of Saturday to join the official process.
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