The powers of Johannesburg's Group Forensics and Investigation Services (GFIS) have been given to the City manager, Floyd Brink.
This came after a behind-closed-doors report at the 13th Ordinary Sitting of Council on Wednesday.
The report was item 17 of 19, which took council until 21:00 to get through.
It said the "investigations conducted by the GFIS were neither compliant with the local government disciplinary regulations for senior managers, nor compliant with the approved GFIS delegations of authority".
The report was adopted by the Government of Local Unity, the name given to the African National Congress (ANC), Economic Freedom Fighters (EFF), Patriotic Alliance and minority party coalition. The GFIS was created by the Democratic Alliance (DA), when they took over in 2016, as Johannesburg's anti-fraud and corruption service.
It is also responsible for investigating the theft of assets, vandalism, maladministration, illegal connections, breach of security, and hijacked properties.
In 2022, the GFIS commissioned the law firm, ENSafrica, to investigate irregularities related to the approval of a R320-million public safety transaction.
The ENSafrica report found Brink did not act when he discovered the multimillion-rand transaction had been pushed through without following due process. Brink was voted in as the City manager in February.
On Tuesday, the DA approached the Gauteng High Court in Johannesburg to reverse this decision.The DA's Belinda Kayser-Echeozonjoku said the conflict of interest in Wednesday's decision was "surreal in its irregularity".
"The highly irregular adoption of the report also creates the unacceptable and illegal situation where the current City manager... whom the DA is litigating to have declared unlawfully appointed, is responsible for making key decisions even where he himself is the subject of possible investigation," she said in a statement on Thursday.
She said the report on GFIS was "devoid of truth and riddled with error", adding, "This report... effectively reverses all the work done by the GFIS taskforce by giving the City manager the power of prosecutor, investigator, judge and jury over matters of corruption and criminality."
Kayser-Echeozonjoku said the DA was seeking urgent legal advice on the matter.
Responding to queries by News24, the mayor, Kabelo Gwamanda, welcomed the resolutions and said it strengthened the GFIS by "regularising its operations and investigations".
Gwamanda said the report "laid bare serious irregularities in how GFIS conducted allegations and investigations against senior City officials and councillors".
He claimed the previous administration, led by the DA, had abused the department by using it to harass officials.
"Several investigations of allegations against councillors were undertaken without following the due and legal process requirements."
He said the allegations against the City manager and senior managers must be approved by council, which he said was following the requirements of the Disciplinary Regulations for Senior Managers, issued in terms of the Municipal Systems Act.
On Wednesday, Brink was mandated to handle any litigation which stemmed from investigations into these "rogue investigations".
Brink has also been mandated to appoint a senior counsel "in cases where there are cases of litigation against the City, and for senior counsel to advise on any other actions which must be taken to remedy the prejudice caused by the abuse of investigative powers and unlawful investigations".
Gwamanda said the City was committed to accountability and consequence management, but in a lawful manner.