President Jacob Zuma's support for an amendment to the Criminal Procedure Act was not meant to be translated into a licence to shoot randomly, his spokesperson said on Monday.

This was in reaction to an apparent botched police shooting in Mabopane, Pretoria at the weekend when a woman was killed and two people wounded after police apparently mistook them for a gang of hijackers.

"When the president spoke to the police, he equally warned against trigger happy policemen. His support for tougher action against violent criminals did not translate to a licence for policemen to just go out and shoot people," said Zuma's spokesperson, Vincent Magwenya.

"As unfortunate and regrettable as this [the Mabopane] incident was, it should not take us away from what is the real problem facing all of us... the fact is, we live behind high walls.

"Our houses are fortified in the same manner as military bases - that is if you can afford the cost - you cannot let your five-year-old out in the streets cycling because we are a security conscious society as a result of the violent nature of crimes we see every day."

Magwenya said the president had yet not received full details of Sunday's shooting.

The Independent Complaints Directorate (ICD) confirmed on Monday it was investigating the incident that happened around 5am on Sunday.

"The police were allegedly following up on a stolen/hijacked vehicle, a grey Toyota Corolla, which they had tracked to a nearby filling station.

"At this stage, it seems to have been a case of mistaken identity," said ICD spokesman Moses Dlamini in a statement.

The police apparently mistook a grey Toyota Conquest for the stolen grey Toyota Corolla.

"According to the driver of the grey Toyota Conquest, who survived unscathed, he stopped and tried getting out of the car to see why he was being stopped. Shots were fired at his vehicle from the direction of the police.

"A lady of about 28-years was shot in the head and died instantly. Another occupant of the car, a 31-year-old lady, was shot in the abdomen and right breast. She is currently at George
Mukhari Hospital.

"Another occupant, a man of about 28-years, was shot in the thigh and left arm. He is also in hospital."

The ICD had taken over the investigation and dockets for murder and three for attempted murder had been opened.

Eight firearms were confiscated and would be sent for ballistic tests.

Police spokesperson Captain Julia Claassen said members of the Flying Squad had been "looking out" for a hijacked grey Toyota Corolla when they spotted a car fitting the description.

"The police put out their blue lights for the driver to stop, but he didn't, so police fired shots," she said.

However, the driver, Simon Mathibela, a captain in the Air Force, told Talk Radio 702 on Monday morning the police's version was not true.

"I am a pilot. I am tested for my hearing. There were no sirens; there was one flash of blue lights and shots fired and my friend is dead."

He said he partly blamed Zuma for the incident.

"The President made a mistake by giving police powers that he could not control," Mathibela said.

However, Zuma's spokesperson said the President never used the words "shoot to kill" in his recent meeting with about 1000 police station commanders to hear from them what problems they faced daily.

This is a phrase that has been coined by some in the media and its use has been very unfair and misleading," Magwenya said.

At the meeting, he expressed support for an amendment to Section 49 of the Criminal Procedure Act that would give the police more leeway to shoot in dangerous situations.

Zuma said at the meeting: "Criminals don't take an oath to do warning shots... If you take a gun out to me, that intent is more than clear, the next thing the criminal is going to shoot at me. That intent is very clear.

"My thinking is once a criminal takes out their gun the intent is clear... police must then act to protect themselves and the innocents... We have an abnormal criminal problem in South Africa. We must therefore apply extraordinary measures," he said.

He did make it clear at the meeting this did not mean police officers should be "trigger happy".

Magwenya said Zuma believed South Africa needed comprehensive measures to deal with crime.

That was why, in the meeting with the police officers, police morale was discussed and Zuma listened to complaints about flaws in the criminal justice system.

However, the government also wanted to send a strong message to criminals.

Magwenya said: "You have criminals who are heavily armed, who have no regard [for] the law, a complete disregard of people's lives, and those criminals need to be dealt with harshly."