Professor Wolfgang Preiser, head of virology at Stellenbosch University, called the mix-up "concerning".
"Figures are vitally important to assess epidemic spread over areas and over time," he said.
The process might be imperfect - "for example undercounting if possible cases aren't even tested, like now again in the Western Cape due to lab overload" - but statistics were needed on the number of people tested, how many were positive, how many were admitted to hospital and so on, so that hotspots could be identified, among other things.
Gauteng released its latest figures on Thursday. They show that as at December 16, the province had 11,369 active Covid-19 cases, with 1,534 people in hospital, compared with 5,021 Covid hospital admissions in July, when SA recorded its first peak of infections.
Kekana said the province had developed plans in preparation for a possible second wave, including better contact tracing.
"We will focus mainly on the trajectory of cases within the districts and identified hotspots as they relate to Gauteng."
Kekana said the provincial health department had conducted an aggressive recruitment process during the first phase of the pandemic to ensure it would have enough staff.
The department would continue to assess the second wave and would do all it could to address potential staffing gaps.