The crackdown on Egypt's Muslim Brotherhood continues just days after 51 people were killed by Egyptian security forces at a protest organized by supporters of ousted President Mohammad Morsi.

On Wednesday, officials confirmed to ABC News that an Egyptian prosecutor ordered the arrest of Brotherhood spiritual leader and "general guide" Mohammed Badie for "inciting violence" at Monday's massacre outside the Egyptian Army's Republican Guard officers' club in Cairo.

Many Brotherhood members have already been hauled in by Egyptian security and warrants have reportedly been issued for hundreds more, including Essam El Erian, the vice chairman of the Brotherhood's political arm, the Freedom and Justice Party.

The arrest warrants follow the Brotherhood's expected rejection of interim President Adly Mansour's path to restoring democracy, calling the Army generals "dictators." The main opposition to Morsi's Brotherhood, the National Salvation Front, also condemned the road map but did not flat-out reject it.

As of now, charges have not been filed against Morsi personally and he has not shown his face since the release of that bizarre YouTube video the night of July 3.

Egypt's Foreign Ministry spokesman Abdel Ati told reporters Wednesday, "[Morsi] is not charged with anything up till now… The public order is at stake right now! People are inciting their followers to go to be martyred, to break inside into military establishments."

As for his whereabouts, Ati only said Morsi is in a "safe place," being treated in "very dignified manner."