The ministry did not say how many of protesters were injured in the latest clashes, but they are thought to be in the dozens.
Several dozen protesters are staging a sit-in in Tahrir, vowing not to leave before Morsi rescinds his decrees. The two sides have called for rival massive protests on Tuesday at two Cairo locations less than a mile apart, raising the possibility of renewed clashes between supporters and opponents of Morsi.
In the latest sign of the unrest sweeping the country, suspected militants blew up a military installation under construction in the central Sinai Peninsula area of al-Qaseema early Sunday, wounding three workers, according to security officials speaking on condition of anonymity because they were not authorized to brief the media.
It was the second blast to target a military building in Sinai in as many days. On Saturday, another border guard structure under construction was blown up in Rafah, close to the Israeli border.
There was no immediate claim of responsibility in either attack, but authorities have been battling al-Qaeda-inspired militants in Sinai who have stepped up attacks against Egyptian security forces, and even on occasion staged cross-border raids targeting Israelis.