In the Maadi neighborhood of Cairo, someone also damaged the offices of the Freedom and Justice Part, the ministry said.
The scene was calm, but tense, outside the presidential palace in the capital, where the military parked tanks and armored personnel carriers, put up barbed-wire barricades and deployed soldiers.
In what looked like a war zone, piles of rubble and burned cars littered the streets and doors of nearby storefronts were smashed in.
Morsy also suffered a hit closer to home Thursday when Rafik Habib, the deputy head of the Freedom and Justice Party, resigned, party spokesman Ahmed Sobe said. Habib did not give a reason.
His resignation brings to five the number of presidential advisers who have left in the last two days. It is the first, however, from the Freedom and Justice Party.
Egyptian judges and media organizations also have staged strikes to show their displeasure with the situation. And 11 organizations representing lawyers, journalists, writers, actors, musicians and tour guides said Morsy and the Muslim Brotherhood were behind the violence, al-Ahram reported.
The group said it would call for Morsy's ouster if the administration failed to protect protesters and "fulfill the aspirations of the January 25 revolution," the newspaper said.
Vice President Mahmoud Mekki asked critics Wednesday to submit their proposals for improving the constitution, and Morsy invited political opponents to a meeting Saturday at the president palace.
But Morsy hasn't said he's ready to alter the constitution or the planned referendum date. And some Muslim Brotherhood officials have been more steadfast, as well as derogatory toward the opposition.
Muslim Brotherhood Secretary-General Mahmoud Hussein said Thusday protesters weren't interested in democracy. He accused them of using "crude and contemptible ways of expression, rather than (putting) their points across in a civilized manner."
While insisting he respects Egyptians' right to peaceful protest, Morsy spent a significant portion of his Thursday night speech blasting those he claims are behind the recent violence. He accused unspecified foreign and domestic sources of funding and fomenting the unrest, making specific reference to "corrupt" opposing forces tied to Mubarak's government.
"The deposed Mubarak regime will not be brought back to life under any circumstances," Morsy said, tweeted the Muslim Brotherhood.