South African National Roads Limited (Sanral) insisted on Tuesday it was not bullying motorists into registering for e-tolling.
The roads agency also described a legal challenge against e-tolling as "unfortunate", saying it should not deter motorists from buying e-tags.
Sanral on Friday revealed penalties for drivers without e-tags will be up to three times higher than normal rates.
On March, the Opposition to Urban Tolling Alliance took Sanral and others to court, claiming consumer rights were being violated.
But Sanral's Nazeer Alli said the courts will rule on this.
“As far as the legal case is concerned, it is a bit unfortunate that people have taken that particular route so late in the day, when they have known about the improvements to the Gauteng Freeway Project.”
Meanwhile, National Consumer Commissioner Mamodupi Mohlala confirmed she will look into complaints about the latest punitive rates.