The Iraqi military has imposed a curfew in the city's heavily secured Green Zone after demonstrators stormed the area. The protests were centered around the state's inability to remove corruption and improve security.
The Iraqi capital's Green Zone houses the parliament, government buildings and many foreign embassies.
The Baghdad Operations Command also blocked several roads to prevent more protesters from entering the city.
The order followed shortly after hundreds of demonstrators protested against the government's failure to approve anti-corruption reforms and to provide security.
"Infiltrators exploited our forces' preoccupation with preparations for the Falluja battle to infiltrate state institutions and cause chaos," the Joint Operations Command said, referring to the battle to reclaim Falluja, west of Baghdad, from "Islamic State" (IS) control.
Security forces responded with tear gas, and reportedly with live fire. Eye witnesses told the dpa news agency that at least three demonstrators were killed and 22 injured. There was no official confirmation of the report.
Friday's protests included supporters of the influential Shiite cleric Moqtada al-Sadr and some other groups. Al-Sadr and his supporters had also participated in a similar protest on April 30, storming the parliament and calling for more security in the wake of bombings claimed by the terror group IS.
Iraq has been experiencing a political deadlock since February this year, when Prime Minister Haider al-Abadi said he would appoint a cabinet of independent technocrats. The move was supposed to help root out corruption.
Shiite leader al-Sadr approves of the prime minister's plan, but has accused other political groups of blocking the proposal and contributing to the impasse. Prime Minister al-Abadi has meanwhile warned that the deadlock could hamper Iraq's fight against IS, which has occupied much of the country.
mg/msh (dpa, AP, AFP)