Maliki seems to be saying the army will not pursue the Mehdi Army for now
Iraqi Prime Minister Nouri Maliki has ordered a stop to all operations against "people who carry weapons" in the country.
This comes a day after he promised to continue to pursue criminals and outlaws in all provinces.
Last week there was intense fighting between the Mehdi Army militia and the Iraqi security forces in Basra.
Separately, police say a suicide bomber killed at least 15 people in an attack in a funeral in the province of Diyala.
The attack, on the funeral of a Sunni policeman, happened in the town of Sadiya, 60km (37 miles) from Baquba.
Attacks on funerals are usually blamed on al-Qaeda in Iraq.
The clashes between the army and Shia militia spread to various areas in Iraq, including Baghdad, and hundreds of people were reported killed in days of fighting.
This eased on Sunday when Shia cleric Moqtada Sadr ordered his Mehdi Army fighters to stand down.
The BBC's Crispin Thorold in Baghdad says Mr Maliki's intentions over the past 10 days have been far from clear.
From the beginning, the prime minister said that the Iraqi security forces operations in Basra were targeting "criminals".
In practice that meant militiamen from the Mehdi Army.
When the Iraqi forces faced tougher resistance than expected, Mr Maliki vowed to continue the fighting to the end.
Instead elaborate negotiations involving, senior Iraqi politicians and the Iranian government, persuaded Moqtada Sadr to back down.
His militia are off the streets, but still have their weapons. Mr Maliki appears to be saying that they will not be pursued, for now, our correspondent says.
Violence continued in the southern city of Basra on Thursday. A US statement said Iraqi troops killed seven militants and detained 16 in clashes.
One of those detained was a militia leader, the statement said, involved in the kidnapping and murder of Iraqi soldiers, oil smuggling and running foreign fighter networks.
In a separate clash, US warplanes bombed insurgents engaging Iraqi forces in Basra, the statement said.
Separately, an American intelligence report on security in Iraq says the improvements seen since the surge in troops last year have been maintained.
The latest National Intelligence Estimate highlights how Sunni Muslim tribes have helped weaken al-Qaeda in Iraq.
The new report was given to Congress a week before the most senior US general in Iraq, David Petraeus, gives evidence to a Senate committee.
The report does not mention the Iraqi government's operation against the Shia groups.