Iraqi Prime Minister Maliki has ordered militants in Basra to lay down their arms within 72 hours.
A spokesperson said that if the weapons are not surrendered, 'the law will follow its course'.
It comes as militants loyal to Shia cleric Moqtada al-Sadr clashed with Iraqi security forces throughout Basra for a second day.
At least 40 people have been killed and 200 wounded in the violence, including civilians, gunmen and Iraqi security forces.
Police said heavy gunbattles between the two sides restarted in five districts of the city after a brief lull, as the Iraqi military continued its operation to clear the city of armed gunmen.
Meanwhile, 14 people were killed and more than 140 wounded in clashes between security forces and Shia militants in Baghdad's Sadr City.
The casualties included women and children caught in the crossfire in the clashes, which broke out yesterday.
Many towns and cities across southern Iraq were under a night-time curfew as authorities sought to prevent further outbreaks of violence.
