Sources close to the investigation told News24 that the three were allegedly offered positions by the SAPS to falsely implicate IPID head Robert McBride.
McBride said he and his colleagues had been intimidated, received threats and that there had been attempts to bribe them.
A man was reportedly shot dead during violence protests on Wednesday.
Thato Motale, 30, was shot on Thursday amid violent protests against North West premier Supra Mahumapelo.
Khomotso Phahlane and his wife allegedly received kickbacks in exchange for tenders.
Police Minister Fikile Mbalula on Wednesday applauded the Gauteng Hawks and the Independent Police Investigative Directorate (IPID) following the joint operation on Tuesday.
Johan Burger of the Institute for Security Studies dissects the fraught legacy of the notorious former Crime Intelligence boss.
Independent police investigative directorate (IPID) officials on Tuesday arrested the captain at the department of correctional services in Tshwane. 
Ipid has uncovered a tender scam reportedly involving top police management.
The raid formed part of the investigation into former acting police commissioner Khomotso Phahlane and SAPS contractor Keith Keating.