"The communication was flawed. There was less consultation than we would have liked," CEO Babalwa Ngonyama told the advisory panel on e-tolling and its socio-economic impact in Midrand.
BBC policy head Pule Mokoena told the panel: "I think the view is broadly, it was flawed. Maybe a number of constituencies weren't consulted or were not given enough time. It could have been done better."
He said if Sanral had talked to the public in a non-confrontational way and addressed all issues around e-tolling, it would comply with the system.
Asked by the panel about the SA National Roads Agency Limited's claim that 82 percent of motorists paid less than R100 a month in e-toll costs, Mokoena said this was "surprising".
"We don't have a breakdown if it's private or business. We need to have a breakdown," he said.
The council noted the benefits the improvements to Gauteng's freeways had brought, such as a reduction in intolerance and stress on the roads, which had a positive impact at home and in the workplace.
However, the BBC felt the billing model needed to be replaced as the costs of e-tolling appeared high for Gauteng residents.
Ngonyama said: "We would suggest the fuel levy, which would work much better than the e-tolling system.
"It spreads the burden, it actually becomes longer-term and is limited in costs."
Other funding options the BBC proposed were to keep the current system, but lower costs over a longer period of time, or subsidise the e-toll system.
Ngonyama said South Africa had always shared infrastructure development, so the costs of Gauteng's highways should be shared as well.
"Gauteng is carrying a whole lot of costs that do not necessarily belong in Gauteng," she said.
The costs of e-tolls particularly affected small and medium enterprises, which did not have the resources of large companies.
"They do need the support so they actually prosper," she said.
To this end the BBC wanted small and medium enterprises to be added to the e-toll exclusion list.
Ngonyama suggested that public-private partnerships could play a greater role in infrastructure development.
This would result in more efficiency, and business would know exactly the costs being dealt with.
The panel is focusing on the implications and perceptions of financing the Gauteng Freeway Improvement Project (GFIP) and e-tolls.
The panel will consult organisations and individuals over a month.
Organisations were invited to make submissions on the economic, social, and environmental impacts of the GFIP and e-tolls, and how e-tolling's costs and benefits were distributed across society and the economy.
The panel was expected to report to premier David Makhura at the end of November.