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The clashes erupted when police and army personnel tried to arrest Shi'ite cleric Mahmoud al-Sarkhi around midnight on Tuesday in the southern city of Karbala, an Interior Ministry intelligence officer and a police witness told Reuters.
Sarkhi and his armed followers have clashed in the past with U.S. forces, Iraqi security forces and supporters of Grand Ayatollah Ali al-Sistani, the most revered Shi'ite cleric in Iraq.
Security forces said they went to arrest Sarkhi after his supporters started blocking roads and manning checkpoints around his neighbourhood in the Shi'ite shrine city, home to the tomb of Imam Hussein, which millions of Shi'ite pilgrims flock to annually.
Sarkhi had published a letter on his website earlier this week criticizing Sistani's decree for Iraqis to fight alongside the security forces against Sunni militants.
Sistani issued his decree after the Islamic State in Iraq and the Levant (ISIL) swept across parts of northern and western Iraq. The group, which rules swathes of territory in an arc from Aleppo in Syria to near the western edge of Baghdad in Iraq, has since shortened its name to Islamic State and declared a "caliphate" to rule over the world's Muslims.
Police and troops reinforced by five helicopter gunships surrounded the house but were prevented from entering by Sarkhi's armed followers, the sources said, adding five police officers and about 40 of Sarkhi's supporters were killed.
The sources said that when security forces managed to break into the house after six hours of clashes, they found Sarkhi had escaped during the battle. Sarkhi's supporters posted on the cleric's website a picture of an Iraqi military Humvee vehicle they said they had destroyed in the battle.