“It’s false to say that the investigation has been completed, it’s still ongoing, it’s at an advanced stage,” Independent Police Investigative Directorate (Ipid) spokesman Moses Dlamini said.
The Star’s deputy editor Kevin Ritchie said the paper stood by its story.
The newspaper reported that Dlamini said the Ipid had completed its investigation into allegations that Phiyega alerted Western Cape police commissioner Lt-Gen Arno Lamoer about an investigation against him.
Dlamini reportedly said the investigating officer had concluded the investigation but needed a week to “tie up loose ends”.
Dlamini said he did not say the investigation had been completed.
Phiyega is accused of alerting Lamoer about an investigation into his reported links with an alleged drug dealer.
The Ipid started probing the matter in October.
Ritchie said: “He’s entitled to his views, it’s obviously different from our recollection of the story.”