The pro-Morsi coalition that called for the protests said it would also hold a rally on Monday outside the court where Morsi is expected to appear.
The Coalition, which demands Morsi's reinstatement, also called for rallies across Egypt starting on Friday.
Police have arrested 60 protesters till now, a security official said.
The clashes came a day after police arrested 20 female Islamist activists in Alexandria after they scuffled with bystanders during a protest, another official said.
In the Nile Delta city of Zaqaziq, five people were also wounded when pro-Morsi protesters clashed with civilian opponents, the official MENA news agency reported.
In Cairo, several hundred Islamists protested outside the main presidential palace as soldiers and police looked on, an AFP correspondent said.
Interior ministry officials say 20,000 policemen will be deployed on Monday to guard the south Cairo academy hosting the trial and to secure Morsi's transport to the makeshift court room.
"The mass rally on Monday... should be outside the (Police Officers' Academy) building in Tora," the Anti-Coup Coalition, which is led by Morsi's Muslim Brotherhood, said in a statement.
Morsi, held at a secret location since the military overthrew him on July 3, is charged with inciting the murder of protesters outside the presidential palace in December 2012.
He is to be tried along with 14 other defendants.
The Islamist's supporters have been battered by a police crackdown since his ouster. About 1,000 people have been killed in clashes and more than 2,000 arrested.
The campaign of arrests of Islamists has left much of their leadership in jail and restricted their ability to organize mass protests.
NJF/NJF