Officials said more than 500 people were injured in the confrontations that began Sunday and lasted until dawn Monday, Ahram Online reported. Two of the dead are police officers. Another man was shot in the head and remains in critical condition, officials said.
Protesters set the Port Said security directorate and governorate headquarters on fire when they hurled Molotov cocktails at the structures.
The injured included 43 people wounded by gunshots and 300 hit by tear gas, officials said.
Demonstrators were protesting an Interior Ministry decision to transfer 39 prisoners from the Suez Canal city elsewhere, and the death sentences for 21 defendants in the first round of sentencing in a case arising from a soccer stadium riot that killed 72 people in February 2012.
Another round of sentencing is scheduled for this week.