Johannesburg's acting city manager, Bryne Maduka, escaped an arrest warrant in December when a customer went to court over their municipal bill.
According to Mayor Mpho Phalatse's spokesperson, Mabine Seabe, the matter pertained to overcharges on a customer's municipal account.
The customer got a court order to compel the City to repay the overcharge.
But, Seabe said officials believed City should contest the order.
The court upheld the original order and authorised a warrant against Maduka.
"However, the matter was settled prior to the execution of the warrant."
Seabe said Maduka was the subject of the warrant "only because he is the City's accounting officer".
The recruitment process for a new city manager is yet to be finalised.
Maduka became the acting city manager in July last year after Floyd Brink was placed on special leave in April.
This followed allegations of misconduct and flouting of procurement processes.
The allegations were over a deal for CCTV equipment for the public safety department worth R320 million.
Before Maduka acted in the role, both Tiaan Ehlers (environment and infrastructure services) and Mesuli Mlandu (city manager's office) had filled the acting city manager role.