Sanral is not retrenching its employees and has not issued retrenchment letters, it said on Friday.
"It is very mischievous of Cosatu to claim that the SA National Roads Agency Limited is retrenching 1200 workers when we only have a staff complement of 283," said Sanral spokesman Vusi Mona in a statement.
On Thursday, Congress of SA Trade Unions Gauteng secretary Dumisani Dakile claimed the e-tolling system was facing a crisis because many workers were being retrenched by Sanral, and the agencies and labour brokers it uses.
"We have confirmed more than 1200 have been retrenched at Sanral. As we speak now many of the workers now at Sanral have received retrenchment notices," Dakile told reporters.
Mona said a service provider for Sanral, the Electronic Toll Company (ETC) was "downscaling" its operations in line with its business model.
"Sanral cannot be held accountable for the business decisions made by its service providers," said Mona.
"Service providers to Cosatu are not the federation and when they retrench, for whatever reason, that can't be equated to Cosatu retrenching its employees."
Mona said it was regrettable that in its opposition to e-tolling Cosatu was misleading the public.
"Even opponents are expected to stick to certain minimum standards of truth," he said.