The move comes amid allegations that al-Mahdi army fighters fuelled the violence in Karbala.
Iraqi security officials had blamed the militia for attacking men guarding mosques in the city, some of whom are linked to the rival Badr Brigades.
Ahmed al-Shaibani, a spokesman for al-Mahdi army, denied that the militia's members were involved.
In a separate incident on Wednesday in Mosul to the north, armed men raided an Iraqi police checkpoint on Wednesday and killed five policemen and a civilian, police said.
A spokesman for al-Maliki said on Wednesday that he had arrived in Karbala to inspect the situation.
The prime minister said on Wednesday that his troops had restored calm to the city and blamed "outlawed armed criminal gangs from the remnants of the buried Saddam regime" for the violence.
"Had the US foreign policy makers read history, they would not get involved in any war after Vietnam"
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However, the violence among rival Shia factions appeared to have spread overnight.
Fighters attacked the offices of a powerful Shia party in at least five cities, setting many of them ablaze.
Al-Maliki, in a statement, said: "The situation in Karbala is under control after military reinforcements arrived and police and military special forces have spread throughout the city to purge those killers and criminals."
Sporadic and occasionally sustained gunfire could still be heard after dawn in the city, coming from the area around the shrines of Imam Hussein and Imam Abbas.
The fighting killed 52 people and wounded 206 on Tuesday, a senior security official in Baghdad said.
The general director of the al-Hussein hospital in Karbala, 110km south of the capital, said it had received 34 bodies and treated 239 wounded.
Ali Kadhum, an official at the shrines' media office, said the two shrines had been slightly damaged, with bullets hitting their domes and minarets and an electric power station ruined.
Hundreds of thousands of pilgrims had gathered in the city to mark the birthday of the 12th and last Shia imam.
The interior ministry accused al-Mahdi army, a militia loyal to Muqtada al-Sadr, the Shia leader, of attacking government forces in Karbala, the site of two shrines under the control of the Supreme Iraqi Islamic Council (SIIC).
Al-Sadr's forces are vying with the SIIC for power in the regions south of Baghdad.
Plea for calm
Police said SIIC buildings were torched overnight in Baghdad's Kadhimiya neighbourhood, in the city of Kufa, in Iskandariya and in al-Hamza district of Babil province.
Another SIIC headquarters was struck by rocket-propelled grenades in the centre of Najaf.