A five percent increase has been approved for local government officials in 278 municipalities, which will cost taxpayers around R90 million, the Sunday Times reports.
Executive mayors of the country's eight metropolitan municipalities, who all earned above R1m per annum, would also get pay hikes.
The determination of salary increases was published by Co-operative Governance Minister Lechesa Tsenoli last week.
The salary increases for councillors include insurance in case they are attacked during a riot or outbreak of public disorder.
This followed the R45m increase for ministers, premiers and high ranking MPs approved by President Jacob Zuma this year, despite a recommendation that all public office bearers earning above R1m not get increases.
Chairpersons of committees at the country's smallest municipalities will get a minimum annual salary of R439 546. Members of mayoral committees in the biggest councils will get a maximum of R883 158.
The recommendation was made by the Independent Commission for the Remuneration of Public Office Bearers.
Municipal IQ, a web-based data service that monitors the performance of the country's municipalities, said the high salaries of councillors showed why these positions were highly sought after.
“Full-time councillors are being very well compensated,” managing director Kevin Allan was quoted as saying.
“In those councils which have experienced multiple protests... one could really question what value a council is receiving for such significant salaries.” - Sapa