Al-Sadr said the crackdown would not work because US forces were involved.
"There is no benefit in this security plan because it is controlled by the occupiers," said an aide to Sadr, reading a statement from the cleric in front of thousands of chanting supporters in the firebrand's stronghold of al-Sadr City.
"(The United States) is watching car bombs explode, taking the souls of thousands of innocent Iraqi people."
Al-Sadr led his Mahdi Army militia in two uprisings against US forces in 2004.
The militia has avoided any confrontation with US forces this time and there was no indication in al-Sadr's statement that this position would change.
They control the College of Administration and Economics, where most of Sunday's deaths occured, the day after al-Maliki said sectarian killings had fallen as a result of the security crackdown.
In Washington, Condoleezza Rice, the secretary of state, urged the Democratic-controlled US Congress not to interfere in the conduct of the Iraq war and suggested president George Bush would defy troop withdrawal legislation.
But Senator Carl Levin, Democratic chairman of the Senate Armed Services Committee, said legislators would step up efforts to force Bush to change course.
"Peace in Iraq will happen when citizens realise that they can express their ideas and views more effectively... than with violence"
JBernar5, Toledo, USA
Send us your views
"The president needs a check and a balance," said Levin.
Rice said on Sunday that proposals being drafted by Senate Democrats to limit the war amounted to "the worst of micromanagement of military affairs."
She said military leaders such as General David Petraeus, the new US commander in Iraq, believe Bush's plan to send more troops is necessary.
"I can't imagine a circumstance in which it's a good thing that their flexibility is constrained by people sitting here in Washington, sitting in the Congress," Rice said.
The Senate Democrats' legislation would try to limit the mission of US troops in Iraq by revoking Congress' 2002 vote authorising Bush's use of force against Saddam Hussein.
Democrats have acknowledged that the proposal does not yet have enough votes to overcome Republican procedural obstacles and a veto by Bush.
But they are hoping the latest effort will draw enough Republican support to embarrass the president and keep the pressure on.
Sensitive to wavering Republicans, Rice made clear that Bush had no intention of backing away from plans to send 21,500 more combat troops to Iraq.