The violence is the latest since protests in Iraq reignited last week after a brief lull amid soaring tensions between Washington and Tehran.
At least three Iraqi protesters were killed on Monday in Baghdad's Tayaran Square after security forces used tear gas and live ammunition, security and medical sources.
One protester was shot by a live bullet in the head, while the second was hit by a tear gas canister, the sources said. Both succumbed to their wounds in the hospital, they added.
In Baghdad's Tayaran Square overnight, protesters threw petrol bombs and stones at police who responded with tear gas and stun grenades, Reuters witnesses said.
Elsewhere in southern Iraq, hundreds of protesters burned tyres and blocked main roads in several cities, including Nassiriya, Kerbala and Amara.
They say Prime Minister Adil Abdul Mahdi has not fulfilled promises including naming a new government acceptable to Iraqis.
"They [security forces] should stop shooting and aiming, who are they and who are we? Both sides are Iraqis. So why are you killing your brothers?" said one woman protester in Baghdad who declined to give her name.
Baghdad police said its forces had successfully reopened all the roads that were closed by "violent gatherings."
Mass protests have gripped Iraq since October 1, with mostly young protesters demanding an overhaul of a political system they see as profoundly corrupt and as keeping most Iraqis in poverty.
More than 450 people have been killed.
Numbers had dwindled but protests resumed last week as demonstrators sought to keep up the momentum after attention turned to the threat of a US-Iran conflict following Washington's killing of Tehran's top general in an air strike inside Iraq.
The killing of Qasem Soleimani, to which Tehran responded with a ballistic missile attack on two Iraqi military bases, has highlighted the influence of some foreign powers in Iraq, especially Iran and US.