Three people died and 15 were injured in Mosul and at least two died and 22 were injured in the northern town of Hawija, the BBC reported, citing police sources.
Soldiers blocked every road leading into Baghdad and traffic was banned downtown.
Protesters threw rocks at police and tried to topple barriers blocking a bridge leading to a square, the BBC reported.
The governor of Basra, an oil city in the south, told about 10,000 protesters he would step down. Iraqi television said he agreed to resign at the request of Prime Minister Nouri al-Maliki.
In a nationally televised speech Thursday evening, Maliki tried to get Iraqis to call off the protests, blaming them on followers of the late Saddam Hussein.
"They are attempting to crack down on everything you have achieved, all the democratic gains, the free elections, the peaceful exchanges of power and freedom," Maliki said. "So I call on you, from a place of compassion, to thwart the enemy plans by not participating in the demonstrations tomorrow, because it's suspicious and it will give rise to the voice of those who destroyed Iraq."
"What happens today will have an important bearing on Iraqi politics over the next six months," Zaid al-Ali, who was a legal adviser for the United Nations in Iraq from 2005 to 2010, told The New York Times.