Strike action is expected to disrupt Metrorail services on Monday, the company said.
"One of the trade unions within the PRASA [Passenger Rail Agency of SA] (including Metrorail) will be embarking on a strike over the salary negotiations process," said Metrorail spokesman Sibusiso Ngomane in a statement on Sunday.
"Metrorail's operations of rail commuters will be affected by the strike."
He said the strike would begin on Monday at one minute past midnight.
"In the event of the strike Metrorail will offer scaled down services of 80 percent in the morning and afternoon peak periods.
He said commuters were therefore encouraged to use alternative transport.
"Metrorail management apologies for the inconvenience caused."
On Friday, the Federation of Unions of South Africa (Fedusa) requested an urgent meeting with Transport Minister Sibusiso Ndebele.
In a letter sent to the minister, the union said it was "dismayed" by the unethical and irresponsible action taken by Metrorail management.
Last week, a strike by the South African Transport and Allied Workers' Union (Satawu) was called off after an agreement was reached.
Fedusa said this placed the company's Utatu members - the majority of its train drivers, operational and maintenance staff - in an "untenable position".
Fedusa general secretary Dennis George said Metrorail had reneged on its previous offer of seven percent from April 1, with adjustments to the housing and medical subsidy which amounted to another one percent, and a further 1.5 percent increase from September 1, which would then total 9.5 percent.
"Their offer of eight percent is therefore ludicrous and is being rejected out of hand by our Utatu members."
George said a "last ditch" attempt to avert the strike by meeting with chief executive officer Lucky Montana had deadlocked.
At the time, he said, intended strike action would have "dire consequences not only for commuters, but also for all other employers in South Africa, as millions of workers will be deprived of their normal means of transport".