It said a meeting had been held between the two institutions to discuss whether public protector Thuli Madonsela would probe the allegations.
"It was agreed that the immediate way forward is to engage with Sanral on their current dispute resolution mechanism, in particular making it more efficient," public protector spokesman Oupa Segalwe said.
"It would appear that there are more problems with the billing of unregistered users of e-tolling. However, there are many registered users of e-tolling who have also complained about their bills," he said.
He said the office currently had 22 individual complaints but had been informed that the Opposition to Urban Tolling Alliance (Outa) had more than 1,300.
"A decision on the way forward will be made after an engagement by both the public protector and the National Consumer Commission with Sanral regarding the efficiency of their process of dealing with complaints," Segalwe said.
"It is our preferred option that Sanral has an efficient internal complaints handling mechanism," he said.
The public protector is also "assessing" allegations brought forward by Outa that Sanral saw the Gauteng e-tolling project as a starting point for national e-tolling.
An informant of Kapsch, the Austrian company which designed the system, told Outa the systems at the central operation centre were actually designed for a national programme.
In response Segalwe said: "The matter is still being assessed. Only after this standard process will the public protector be in a position to make a decision on whether to investigate."
Meanwhile, Deputy President Kgalema Motlanthe has officially opened Sanral's central operations centre in Midrand.
The entire Gauteng freeway management system is operated from the centre which has 1,300 employees.
Source: Sowetan via I-Net Bridge
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