Emergency services official Amr Salama says the 12 died when hundreds of Islamists descended on a rally by opponents of ousted President Mohammed Morsi in the city, opening fire with guns.
He says clashes erupted, and police joined on the side of the Morsi opponents.
Salama says he saw one man die when he went to the roof of a building, raised an Egyptian flag and shouted insults against Morsi. Morsi backers went to the roof and stabbed him and threw him off the building.
The state news agency MENA also confirmed 12 dead in the city.
