Cosatu is due to lead a march against e-tolling on Friday.
"Government calls on marchers to exercise their right to protest within the ambit of the law," said spokesperson Thabo Masebe.
The warning followed reports that the Congress of South African Trade Unions's (Cosatu) provincial secretary Dumisani Dakile had stated that they would demolish the tolls if government failed to listen to them and scrap the tolls.
"I think if government doesn't listen, then people will have no choice but to go and demolish those toll-gates," he said at a press briefing on Wednesday.
But, speaking to Eyewitness News on Thursday morning, Dakile said he was misunderstood and explained that he meant to say that government officials who tore down houses in Lenasia several weeks ago should also tear down the tolls.
The houses had reportedly been illegally constructed on land meant for government housing.
The anti-toll protests would be staged on Friday by members of Cosatu and the public in Johannesburg and Pretoria.
Cosatu general secretary Zwelinzima Vavi said this was just the beginning.
"On the 6th of December we are not only going to march, but give the government a little dose of what to expect in March if they pass that law and try to force implementation of the e-tolls," he said.
Government officials said they would be closely monitoring the demonstrations.
Meanwhile, the North Gauteng High Court is yet to deliver its verdict on the fate of the tolls.
The Opposition to Urban Tolling Alliance wants the court to review and set aside the South African National Roads Agency Limited's decision to declare sections of Gauteng's freeways as toll roads. – Sapa