Iraqi police say the powerful Mehdi Army militia has been involved in killing of hundreds of people in the mainly Shia Muslim province of Karbala.
Maj Gen Raid Shaker told a public meeting the militia of radical cleric Moqtada Sadr had brought four years of terror and anarchy causing 670 deaths.
His allegations were backed by scores of angry people attending the meeting.
Mr Sadr's supporters have rejected the allegations, saying they are victims of a smear to cover up excesses by police.
The BBC 's Jim Muir in Baghdad says such direct and public allegations are unprecedented and may indicate growing confidence on the part of the authorities that they can take on the militia.
Mr Sadr suspended the activities of the Mehdi Army for six months in August "in order to rehabilitate it in a way that will safeguard its ideological image".
The allegations came out as part of a bitter war of words that is now raging between police chiefs and the Mehdi Army, our correspondent says.
During the four years to August 2007, Gen Shaker said more than 60 policemen and 600 civilians, including nearly 70 women, had been killed by the militia.
Many participants at the meeting made emotional statements giving details of relatives they said had been killed or tortured by the Mehdi Army.
The Mehdi Army's grip on Karbala - home to some of Shia Islam's holiest shrines - was broken in August after it was blamed for violent clashes with police in which more than 50 people were killed.
Before that, such public accusations against the militia would have been unthinkable, our correspondent says.