Medupi Power Station has proved to be a financial and logistical nightmare for Eskom.
Between 500 and 1 000 striking workers began protest action at the massive-scale coal fuelled plant, which is still under construction.
Reports on Twitter said on Wednesday that several people had been injured in violent confrontation between protesters and the police, but Eskom did not confirm this. "The protest turned violent with stone throwing and damage to two vehicles, but no one was injured as far as we are aware," it said.
Unions and management at Eskom are currently in a deadlock over wage negotiations. The public owned company has offered a wage increase of 5.6% to the workers, but unions have dismissed this as an "insult".
Dissatisfaction with the negotiation process has already led to small-scale protests at four key Eskom power stations, including Matimba, Duvha, Matla and Hendrina over the past two weeks.
Last Friday, leaders from major union representatives the National Union of Metalworkers South Africa and the National Union of Mineworkers warned that unhappiness at other power stations would likely see further work stoppages.
Eskom approached the Labour Court last week in a bid to have any strike action by its employees recognised as unlawful, on the grounds that the company is a "designated service provider". It also asked the court to compel unions to issue a statement urging workers to remain at their posts.
But union leaders said they would do no such thing, and that workers were so angry that such an encouragement would not serve to quell them.
Eskom confirmed that the "majority" of workers at Medupi had been sent off site, but that they are "working to get back to normal operations as soon as possible".
"The situation is under control and calm has been restored on site," it said.
The strike comes just weeks after Public Enterprises Minister Malusi Gigaba announced that the completion of the Medupi plant – which is set to provide 4 800 MW of electricity to the country – will be delayed by at least six months.