He said a terrorist attacked remained unlikely but police had carried out simulations lasting up to a week to train for everything from chemical, radiological and biological attacks to bombs and serious accidents.
"There is no intelligence to suggest there there is any threat of terrorism during the World Cup. South Africa on its own is not a target for terrorism," Naidoo said.
But he added that some of the teams taking part, which might include both the United States and England, could be seen as potential targets. "There is the potential that one or two of those countries may import the threat of a terrorism attack into the country," he added.
"The fact that we are not a target for terrorism does not mean we can remain complacent."
Since the end of apartheid in 1994, South Africa has pursued a strongly independent diplomatic stance and has been outspoken in criticising Western actions in the Middle East and elsewhere.
South Africa has one of the world's highest rates of murder and rape, with about 50 people killed violently every day, slightly higher than the United States with six times the population and crime is a leading concern for World Cup organisers.
Naidoo said a total of 52,000 officers would be on duty to provide security during the competition, more than a quarter of the country's entire regular police strength in a strategy based on saturating areas where fans, teams and tourists are likely to congregate - from stadiums to transport routes.
But he said police were ready for fans to stray away from these areas. "We expect people to go anywhere in South Africa, not necessarily those areas concentrated around stadiums."
Authorities have identified 169 police stations, out of a total of more than 1,100, in areas where more than 50 percent of violent crimes occur. These stations are already being heavily reinforced to try to bring down crime statistics which Naidoo described as "bleak".
The rest of the police force would complement those officers dedicated to World Cup duty and vice versa. "Whichever areas people want to venture into there would be that saturation of uniformed police officers," he said, adding that nearly 40 helicopters would provide overhead surveillance as well.
In response to a question, he said police would not try to block the movement of fans. "To restrict anybody's movements is unconstitutional first and foremost...we are in the business of making sure people who have to venture into any areas will be safe and secure."
French police are training South Africa's force in crowd control for the World Cup in a programme expected to be complete by the end of the year, Naidoo said.
Police are working with Interpol and foreign law enforcement to identify known hooligans and ban them from South Africa.
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