The strike would paralyse freight rail services and impact ports in Africa's most advanced economy.
The state-owned Transnet has been operating below capacity due to a shortage of locomotives, poor maintenance and vandalism and theft of its infrastructure, costing miners billions of rand in potential revenue.
The United National Transport Union (UNTU) and the South African Transport and Allied Workers Union (Satawu), which represent most Transnet workers, turned down Transnet's offer of a wage rise of 3-4%, saying it was below South Africa's annual inflation rate, which was 7.6% in August.
Transnet said the strike was illegal, saying unions had not followed rules set down in the labour law. UNTU and Satawu said Transnet's lawyers had written to them on Oct. 3 saying their industrial action would be illegal as some workers involved provided essential services and were restricted from striking.
Transnet also questioned the unions' balloting processes, through which members approved strike action. It also said no picketing rules had been agreed on by the company and striking workers, as required by the labour law, the unions said.
UNTU and Satawu rejected Transnet's charges, saying they had given the required 48-hour strike notice and engaged Transnet on picketing rules.
Transnet did not respond to a request for comment.
UNTU, which says it is the biggest union at Transnet, confirmed its members began a strike on Thursday morning, while Satawu has said it will join in the strike from Monday.
"This will have a profound impact on economic activity across all sectors, and (Transnet) urges workers to consider the long-term consequences of the strike on themselves, their colleagues, their families and the South African economy as a whole," Transnet said in a statement.
UNTU general secretary Cobus van Vuuren accused Transnet of seeking to intimidate workers by declaring the strike illegal.
"This is just another attempt by Transnet to deploy scare tactics to prevent the strike and to delay the process," he said.
All parties have agreed to mediation by the Commission for Conciliation, Mediation and Arbitration (CCMA), a state agency. The unions have said further talks, due to start on Oct. 12, will not affect strike plans.
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