The protests came after an Islamist alliance that backs Morsi called for demonstrations ahead of a new hearing on Wednesday in a trial of the ousted president.
Police moved in swiftly to disperse the rallies, after warning they would not tolerate protests by Morsi's Muslim Brotherhood following its designation as a terrorist group last week.
Four were killed in Cairo and the rest in several other cities, the ministry said, adding that at least 52 people were wounded. The ministry did not say whether the dead were protesters, police or bystanders. The interior ministry said 122 protesters were arrested.
Protesters in the capital set fire to a police vehicle with petrol bombs, a security official said, with state media saying residents extinguished the fires.
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In the upscale neighbourhood of Maadi, police fired tear gas near a military hospital as protesters threw fireworks at them, an AFP reporter said.
Protesters also clashed with police on a road along the Nile River and inside the suburb.
The street was littered with rocks and burning wood as police vehicles sped up and down the road to disperse the protesters.
The demonstrators regrouped in a side street, facing off with riot police and chanting "They are the thugs!". Some protesters threw stones.
Gunshots were also heard.
Protesters chanted "Down with military rule" and slogans against army chief Abdel Fattah al-Sissi, who led Morsi's ouster in July.
Cairo's main squares were sealed off by security forces with barbed wire and military vehicles.
They included Tahrir Square, as well as Rabaa al-Adawiya and Nahda squares, which were the sites of a bloody crackdown on Morsi's supporters in August.
State news agency MENA reported a number were wounded by birdshot in clashes in Alexandria and that Morsi supporters set fire to two civilian cars.
More than 1,000 people, mostly Islamists, died in street clashes following his overthrow, and thousands have been imprisoned.