"Treasury has made it very clear they didn't plan for this, it can't be expected to step in," Jeremy Gauntlett told the court, appearing in behalf of national treasury.
The government and the South African National Roads Agency Limited (Sanral) are currently squaring up against the Opposition to Urban Tolling Alliance (Outa) as they appeal an interdict granted by the North Gauteng High Court against the introduction of e-tolling in April.
Rating agency Moody's previously warned the continued indecision over the implementation of e-tolling threatens South Africa's credit rating.
Gauntlett argued Outa's opposition to e-tolling is akin to witnessing a hospital being constructed, but waiting for its completion to raise concerns about how it is being funded.
"The respondent's argument that Sanral is not ready to charge for tolling is untrue. They indeed are and the longer they are prevented from doing so the more dire the situation will become," he said.
The Sanral project aims to see Gauteng's road users billed electronically when using the province's highways. The tolling requires commuters to fit an e-tag which will monitor the number of times they pass a specific gantry on the highway, and will then charge them accordingly. Cars without e-tags will have their licence plates monitored and billed for their journeys.
A full judicial review of the decision to implement e-tolling is set to be heard in the North Gauteng High Court from November 26.
But Gauntlett said the review should have been expedited to finalise the matter, instead of implementing an interdict that threatens South Africa's economic future.
Gauntlett said government will be forced into a position where they "have to rob Peter to pay Paul" in order to fund the costs incurred through the road improvements.
"At a time of massive deficits in other parts of the world, the North Gauteng High Court didn't take into account the impact of preventing e-tolling from being implemented," he added.
After a brief recess, David Unterhalter took over arguments for Sanral and immediately began discounting Outa's suggestions of alternative funding models.
Unterhalter said treasury made a conscious decision not to use a dedicated fuel levy to fund the building of roads, as suggested by Outa.
"All concerns were taken into consideration, and the best funding model was decided upon. It's hard to see how a court review of the decision to implement e-tolling will change the fact that it's the best system available," he said.
The case continues and arguments will be heard from Alistair Franklin SC on behalf of Outa later on Wednesday.
Meanwhile, during proceedings a group of approximately 50 Democratic Alliance supporters protested outside court.
"Phansi, e-tolling! Phansi!" protesters cried as they waved placards and toyi-toyed.
"We are here to show our opposition to the continued push to implement e-tolling. Government is trying to ram this system through without proper explanation,' Jack Bloom, DA leader in the Gauteng legisalture, told the Mail & Guardian.
The opposition party failed in its bid to join the case on Gauteng's e-tolling as part of the respondents.