The former Vosloorus Police Station commander on Friday accused Richard Mdluli of lying to him about his involvement in the murder of Oupa Ramogibe more than a decade ago.
The accusation was made during the inquest into Ramogibe's death at the Boksburg Magistrate's Court.
Former Crime Intelligence head Mdluli was charged with the murder of Ramogibe.
But in February, the National Prosecuting Authority (NPA) withdrew the charges, pending the outcome of the inquiry.
Colonel Johannes Manyathela said two hours after Ramogibe was murdered, Mdluli approached him with an explanation of what happened.
Manyathela said the following day, Ramogibe's family told him about the threats Mdluli had made against Oupa.
The family had said both Mdluli and Ramogibe were romantically linked to the same woman.
Manyathela said he referred the matter to the area commander and at the time believed the murder docket was in good hands.
He told the court he came forward to help police when he realised in 2010 that the case was not being properly investigated.
Manyathela said he felt that Ramogibe's family told him the truth, and that Mdluli lied to him in 1999.
The murder inquest continues in court.