President Jacob Zuma said on Friday that the police did not have a licence to kill.
"I have noted continuing media reports about the use of force by the police, which has at times led to the tragic loss of life, including the lives of children," Zuma said in a statement.
"No police officer has permission to shoot suspects in circumstances other than those provided for by law. The law does not give the police a licence to kill."
Reports of civilians being shot dead by the police have increased sharply since Zuma and some of his ministers urged the police to take a tougher line on dealing with criminals.
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In a recent case, a police constable was arrested for allegedly shooting dead three-year-old Atlegang Aphane in Midrand. The constable had apparently mistaken a metal pipe the child was holding for a gun.
In a speech on Thursday, Deputy Police Minister Fikile Mbalula said it was unavoidable that civilians would die in the crossfire between police and criminals.
"In the course of any duty the innocent will be victimised," Mbalula told reporters at Parliament.
"In this particular situation where you are caught in combat with criminals, innocent people are going to die, not deliberately, but in the exchange of fire. They are going to be caught on the wrong side, not deliberately, but unavoidably.
"Yes. Shoot the bastards. Hard nut to crack, incorrigible criminals."
Zuma said the comments made by government leaders "in no way constituted an instruction to deviate from the law".
"Comments that I and other government leaders have made about the need to clarify the conditions under which police may use lethal force in no way constitute an instruction to deviate from what is contained in law," he said.
"We have stated our position very clearly. It is the duty of the police to protect all people against injury or loss of life.
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