Sanral chief executive Nazir Alli said in a statement the agency had responded to Zuma through the office of the presidency’s director general.
Zuma told the SABC in an interview that e-toll billing mistakes were unacceptable.
“You can’t then bill people wrongly. It is a matter that needs to be fixed, and be fixed very quickly because it undermines an efficient system.”
Alli said complaints about incorrect bills were taken very seriously and the agency was working to correct such problems, some of which had to do with inaccurate data on the national traffic information system.
He maintained that the problem was “not that widespread”, as the e-tolling system processed millions of transactions each day.
“Of course, we appreciate that however less pronounced it may be in relation to the volumes of traffic on the e-roads, both the president and the department of transport would be concerned about citizens not getting the kind of service they deserve.”
He said Sanral was working with its service provider the Electronic Toll Company (ETC) to resolve the problems.
ETC chief executive Jamie Surkont said in the same statement his company had begun case studies on some of the e-tolling complaints highlighted in the media recently.
The findings thus far had “allowed us to consider changes to our customer management; and they have corroborated that the toll system is functioning as designed,” Surkont said.