The health ministry said four people were killed in violence in the Suez Canal city of Ismailiya and another eight in northern Damietta.
Security sources told AFP five protesters had been killed in clashes with security forces in Ismailiya.
And they said a police conscript was killed when gunmen attacked a checkpoint in the capital.
The violence came as Islamists marched in several cities around Egypt in what they dubbed a "Friday of anger" to protest the killing of hundreds of Morsi loyalists following a security crackdown on Wednesday.
Protests were held in Cairo, in the northern city of Alexandria, in Beni Sueif and Fayoum, south of Cairo, and in the Red Sea resort town of Hurghada.
The interior ministry said Thursday that it would take tough measures, including the use of live fire, if protesters attacked government buildings.
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