She has blamed political interference and intimidation.
Lindiwe Msengana-Ndlela has complained that interference by the executive mayor Nkosinathi Benson Fihla and deputy mayor Thando Ngcolomba is making her job unbearable and putting her security at risk.
In a letter requesting the intervention of the MEC for local government and traditional affairs, Mlibo Qoboshiyane, Msengana-Ndlela said: "Regretfully, the city manager's administrative efforts of addressing the supply-chain management challenges and matters raised in the previous report of the auditor general are being thwarted through political interference."
One disagreement relates to the handling of a R174-million tender awarded to Lumen Technologies for equipment to display the end destination for commuters on metro buses. The technology also uses a GPS tracking system to monitor driving behaviour and speed. In awarding the tender, the metro used section 32 of the supply chain management regulations, which allows for the utilisation of a contract secured by another organ of state. In this case, the City of Cape Town had already contracted the company to provide similar services.
A probe commissioned by Msengana-Ndlela apparently found Lumen had inflated prices for the service they were contracted to provide.
In her letter to Qoboshiyane, Msengana-Ndlela said her efforts to put the city's financial accountability on the right path had been frustrated by politicians.
"A case in point is the legal matter on the integrated public transport system between the metro and Lumen Technologies CC and another. The city manager made clear recommendations on corrective measures, which took into consideration the point of law before the courts, the financial implications of the matter and the possibility of securing a negotiated settlement within the relevant legal frameworks."
A source in the municipality close to Msengana-Ndlela said politicians such as the mayor and his deputy were "eager for an out-of-court settlement, citing the importance to save the funds allocated to the [metro bus] project, which will be returned to treasury if it waits for the court process".
But "Lindiwe wants it to go to court given the level of gross irregularities she found".
Other instances of political interference Msengana-Ndlela listed in her letter to Qoboshiyane include:
l Fihla and Ngcolomba had pressured her to appoint a political adviser in the administration as an acting executive director of corporate services, and/or other senior managers irrespective of their competencies, qualifications and experience.
Fihla reminded Msengana-Ndlela of "incidents of violence and death when people don't comply with the 'majority rule' concept", which the municipal manager said was being used to force her to perform administrative acts that were contrary to government policies and procedure; and
l Fihla instructed Msengana-Ndlela to appoint 16 members of the Mkhonto weSizwe Military Veterans' Association (MKMVA) as bodyguards for the mayor and deputy mayor at an estimated cost of R4.3-million, even though there was no budget for the posts.
Msengana-Ndlela wrote that it appeared the MKMVA members had been informed of their appointment, and the veterans were under the impression their appointment was being delayed by the city manager.
"One of the members approached the city manager in her car in the evening, knocking on her window and questioned her about the delays in their appointment. The harassment of the city manager in this manner places her life in danger."
Msengana-Ndlela said she had been "frequently reminded by the executive mayor of the violence and the ultimate price that is paid by those who do not submit to majority rule".
Experience in governance
She said: "How then, would any reasonable person construe these reminders of violence against those who express a different point of view if not as threats against the city manager? Seemingly there is so much at stake that issues of the administration in the metro … that these matters have been turned [into] issues of life and death."
In March the Mail & Guardian reported that ANC members in the Nelson Mandela Bay region had expressed doubt that the removal of then-mayor Zanoxolo Wayile and his replacement with Fihla would improve service delivery or address the infighting that has crippled the party in the region.
At the age of 81, Fihla was promoted from being an ordinary MP to running one of the difficult metropolitan municipalities, despite his lack of experience in governance.
Fihla and Ngcolomba were asked for comment but had not responded at the time of going to print.
According to the auditor general's presentation to the Eastern Cape provincial legislature in December, the procurement of goods and services in the municipality was deliberately split into items of smaller value to avoid complying with the requirements of the supply-chain management regulations and R557.2-million of unauthorised, irregular, and fruitless and wasteful expenditure was incurred during the financial year.
In addition, unauthorised expenditure amounting to R318.7-million was incurred due to overspending in the approved municipal budget. There was also irregular expenditure of R234-million relating to contraventions of the supply-chain management requirements, and fruitless and wasteful expenditure amounting to R4.5-million was incurred due to breaches of contractual agreements.
Under Msengana-Ndlela, the former department of provincial and local government, now called co-operative governance and traditional affairs, received clean audits for seven consecutive years.