Detective Hilton Botha was dropped from the investigation in February after it emerged that he was facing attempted murder charges in another case.
He has also been heavily criticized for giving contradictory evidence at the bail hearing of Oscar Pistorius.
Oscar Pistorius is accused of killing his girlfriend, model Reeva Steenkamp – a charge he denies.
The athlete says he mistook her for a burglar when he shot her dead on February 14.
Reeva Steenkamp, 29, died after the athlete fired multiple shots into the toilet of his apartment in a gated housing complex in Pretoria.
Hilton Botha, the first officer to arrive at the scene of the shooting, was accused of mishandling the investigation after he amended his testimony during fierce questioning by Oscar Pistorius’s defence lawyers in last month’s bail hearing.
It also emerged that the detective was allegedly involved in the shooting of a minibus taxi loaded with passengers two years ago.
The charges against him had originally been dropped but were later reinstated.
Hilton Botha is set to appear in court in May, along with two other officers also accused of opening fire on the taxi.
Police have not commented on the reasons behind Hilton Bopha’s resignation.
Oscar Pistorius, who is charged with premeditated murder, was released on bail on February 22 and is due to appear in court again in June.
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