"We recognise the significance, the importance and the severity of the matter," police commissioner Riah Phiyega said as she announced the appointment of Lieutenant General Vineshkumar Moonoo. "This matter will receive attention at the national level."
The charges against detective Hilton Botha further embarrassed the prosecution which has seen its evidence repeatedly picked apart during the bail hearing for Pistorius over the Valentine's Day killing of his girlfriend Reeva Steenkamp.
Pistorius says he mistook his 29-year-old model girlfriend for an intruder and denies murdering her intentionally.
He suffered a new blow on Thursday when US sportswear giant Nike said it has suspended its contract with the double amputee Olympian and Paralympian known as "Blade Runner" who had become an inspiration to millions.
The 26-year-old is due back in court on Friday for the fourth day of the bail hearing.
Observers think he will be let free pending the trial because prosecutors have struggled to prove Steenkamp's killing was premeditated -- a more severe charge which makes bail hard to get.
After Botha's much-criticised court performance, during which he made contradictory statements and admitted to mistakes at the crime scene, police revealed on Thursday that the lead detective is facing seven charges for shooting at a minibus taxi in 2011.
"The poor quality of the evidence of investigating officer Botha further exposed... the disastrous shortcomings in the state's case," said defence lawyer Barry Roux.
Phiyega said career police officer Moonoo, who has three decades of experience, would take over from Botha in a case that has shone an unflattering light on the competence of the country's police force.
"He is the most senior detective in the SAPS (South African Police Services) environment," she said.
Steenkamp was found by medics in the early hours of last Thursday at Pistorius's luxury Pretoria home covered in bloodied towels, with bullet wounds to her head, elbow and hip. She died at the scene.
The athlete has previously said he kept a gun in his bedroom because of fears of violent burglary.
But prosecutor Gerrie Nel highlighted the extreme nature of Pistorius's actions that night.
"He fired four shots, not one. He meant to kill. On his own version, he's bound to be convicted."
The sprinter, who has been in police custody for a week, could face months or perhaps years in pre-trial detention if he does not win bail.
But Nel warned against giving Pistorius preferential treatment because he's famous.
"'I am Oscar Pistorius. I am a world renowned athlete. Can I get bail.' No, we have to look at the person," Nel said.
In a statement read out in court earlier this week Pistorius said he had fired at the door of the bathroom where his lover was hiding as he was "filled with horrible fear" that someone had sneaked in through an open window in the dead of night.
Under South African law shooting someone without immediate threat is punishable, and Pistorius fired while there was a chance for escape through his bedroom, according to the prosecution.
-- 'It could have been handled better' --
Botha was earlier forced to admit that Pistorius's claims were "consistent" with the crime scene and on Thursday said of the investigation: "I'm sure it could have been handled better."
He has conceded he did not wear protective clothing when the forensic team visited Pistorius's home, which may have contaminated the scene, and that his team had failed to spot a bullet that was discovered four days later by the defence forensic team.
Roux on Wednesday also threw doubt on key prosecution witness evidence suggesting the couple, who had been dating since late last year, had an argument before the shooting.
The lawyer pointed out that police had said one witness was at least 300 metres (nearly 1,000 feet) from the house and the other had misheard the number of gunshots.
Prosecutors also backtracked on allegations that a police search had found testosterone and needles in a dresser in Pistorius's bedroom.
Arguing that Pistorius would be a flight risk, the prosecution quoted a magazine article in which the runner claimed to have a house in Italy.
But his coach Ampie Louw told AFP the property is actually a training facility built by the local government and a hotel, where the athlete goes regularly to train and unwind.
Pistorius's career has been put on hold since the shooting, forcing him to cancel a number of races.
Nike on Thursday became the latest in a series of corporate giants to halt endorsements which have earned the athlete millions of dollars. US sunglasses maker Oakley has already suspended its contract with him and French cosmetics firm Clarins said it was dropping an advertising campaign featuring Pistorius.
The athlete became the first double amputee to compete at an Olympics at the London games last year.
Off the track he has had a rocky private life with stories of rash behaviour, beautiful women, guns and fast cars. He has built up a powerful team of lawyers, medical specialists and public relations experts for his defence.
