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.
Zuma told senior police officials from across South Africa last month he was not encouraging a trigger-happy police force, but he made it clear officers should become far more energetic.
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.
About 50 people are killed in South Africa each day, sometimes for as little as a mobile phone. Violent business robberies climbed by 41.5 percent from April 2008 to March 2009 and house robberies rose by 27.3 percent.
Zuma said fighting crime was a top priority.
"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.
Officials have made it clear that failure to police the World Cup is not an option. South Africa is boosting the size of its police force of 183,000. Its arsenal includes 200 revamped armoured vehicles, 100 high-performance cars for road security, 40 helicopters, and mobile command vehicles.
