Lt. Gen Vinesh Moonoo is to take over the Oscar Pistorius inquiry amid attempted murder accusations against current lead, Detective Hilton Botha.
Detective Hilton Botha was removed pending the result of an investigation into seven counts of attempted murder.
National police commissioner Mangwashi Phiyega announced the change after a third day of testimony at Oscar Pistorius’s bail hearing.
Oscar Pistorius, 26, denies murdering his girlfriend Reeva Steenkamp, 29.
Reeva Steenkamp died after being shot three times at Oscar Pistorius’ home on 14 February.
Mangwashi Phiyega said the police had received feedback from state prosecutors about Det. Hilton Botha only on Wednesday.
She described him as an “experienced detective” who was not yet facing any criminal charges.
However, she said she was using her authority as national police chief to ask Lt. Gen Vinesh Moonoo to take over the Pistorius case.
Vinesh Moonoo is reported to be a veteran of some 30 years service. He will work with the police chief in Gauteng province on a case Mangwashi Phiyega said required attention “at a national level”.
She denied that the decision to replace Det. Hilton Botha was embarrassing for the police.
The claims against Det. Hilton Botha refer to a 2009 incident in which he and several other officers allegedly opened fired on a minibus taxi carrying seven passengers when the driver apparently disobeyed an order to stop.
In court on Thursday, defence and prosecution lawyers offered their final arguments.
The magistrate is expected to issues his ruling on Oscar Pistorius’s bail application on Friday.
Lead defence lawyer Barry Roux asked for the charge of premeditated murder to be downgraded, and said Det. Hilton Botha’s contradictory evidence on Wednesday had undermined the prosecution’s case.
Barry Roux said: “The poor quality of the evidence offered by investigative officer Botha exposed the disastrous shortcomings of the state’s case.”
The defence counsel said the fact that Oscar Pistorius had carried Reeva Steenkamp downstairs showed he was desperate to save her life.
On Wednesday, Det. Hilton Botha told the court that the trajectory of gunshots through the bathroom door indicated that Oscar Pistorius, a double amputee, was wearing his prosthetic legs and shot downwards through the door.
This contradicted an earlier account given by Oscar Pistorius, who said he was walking on his stumps and grabbed his gun because he felt vulnerable when he thought an intruder had entered his home.
But Det. Hilton Botha also amended his testimony on the proximity of the witness who he said had heard arguments.
He said police had lost track of ammunition found inside the house, and was also accused of not wearing protective clothing at the crime scene.
The defence also countered police suggestions that testosterone and needles had been found in Oscar Pistorius’s bedroom, arguing instead that the substance was a herbal remedy called Testocompasutium co-enzyme.
On Thursday, prosecutor Gerrie Nel told the court that Oscar Pistorius should not be granted bail simply because he is famous.
Gerrie Nel branded Oscar Pistorius as a man “prone to violence” who threatened Reeva Steenkamp and eventually killed her.