South Africa has one of the world's highest rates of violent crime and Zuma has appointed a tough talking police chief and made the fight against crime a top priority.
Zuma said in a statement police should act within the law when they are forced to use deadly force.
"However, we expect our police officers to observe the law and respect the rights of innocent citizens, at all times. No police officer has a licence to kill," Zuma said.
Opposition groups criticised his comments, saying it was a sign the government could be taking draconian measures to curb crime.
Police have been criticised after a three-year-old was shot and killed this month.
The country's deputy Police Minister Fikile Mbalula said on Thursday it was inevitable that civilians will be caught in the crossfire between police and criminals.
But Mbalula said police could not back away from a fight with criminals. "Yes, shoot the bastards," he was quoted as saying by South Africa's The Times newspaper.
"Our government has placed crime at the top of its agenda. We want to reduce serious and violent crimes by the set target of 7-10 percent per annum," he said.
