The Department of Transport has given the Road Traffic Management Corporation (RTMC) until today to set up its own payroll system.

The department said the order to the corporation, which has been in existence since 1995, was unrelated to revelations late last week that the agency, which co-ordinates the planning, regulation and facilitation of traffic matters, had failed to transfer more than R200m in fees it owed the department since October.

The RTMC had withheld more than R246m in licensing fees collected via eNatis, the department’ s acting director-general, George Mahlalela, said on Friday.

This was one of several concerns about the troubled agency, which Transport Minister Sibusiso Ndebele said on Friday would be the subject of an inquiry into allegations of financial mismanagement.

The Democratic Alliance (DA) said on Friday the department had decided not to pay salaries to the agency’s employees until it had paid the amount owed to the department for eNatis transaction fees.

Mahlalela, however, denied that the department had frozen salaries of the RTMC’s employees.

That the RTMC, an independent entity, did not have its own payroll system was a “corporate governance lapse”, he said, and the department had instructed the agency last Monday to create its own payroll system .

On eNatis payments, Mahlalela said the agency’s last payment to the department took place in October last year.

For the financial year ending in March, the department had received R150m from the RTMC.

The road traffic agency monitors and collects a portion of transaction fees from provincial departments for annual vehicle licensing transactions. These fees are transferred from the RTMC to the transport department, which in turn passes the fees over to the Treasury.

The money is intended to improve SA’s licence testing systems and implement the Administrative Adjudication of Road Traffic Offences Act .

Asked by the department why payments had ceased, the agency said it had not received payments from the provincial transport departments, Mahlalela said.

Ndebele had ordered an investigation by an independent task team to ascertain why there had been a delay in the payment of eNatis fees. If the probe uncovered serious violations, the department would take disciplinary action, Mahlalela said.

In a statement on Friday, Ndebele said he had received various complaints relating to allegations of mismanagement at the RTMC over the past year.

The DA said on Friday it had requested that the public protector formally investigate the conduct of Ranthoko Rakgoale, CEO of the RTMC, and the agency’s other senior managers following allegations of gross financial mismanagement, procurement irregularities and the misappropriation of funds.