Maliki, a Shia criticised for not doing enough to combat Shia fighters, has vowed to deal even-handedly with citizens from both Sunni and Shia sects.
A statement from Maliki's office reminded security forces to "respect the citizen" during searches.
"We will punish all those who ease up on searches involving people from their sect or ethnicity," the statement said.
Washington has identified the Mahdi Army, a militia loyal to Shia cleric Muqtada al-Sadr, as the greatest threat to security in Iraq.
Sunni Arabs blame it for running death squads. Sadr denies the charge and reportedly fled to Iran as the government crackdown began.
"The prime minister pointed out the positive results that were produced in the last few days after a number of terrorist cells were broken up and many of their operations failed, as well as the return of hundreds of displaced families to their areas," the statement said.