The circumstances were unclear, with management at the Gold One mine near Johannesburg and the National Union of Mineworkers (NUM), one of the two unions involved, saying the miners were being "held hostage."
But the Association of Mineworkers and Construction Union (AMCU) has denied it is keeping workers underground against their will, saying they are staging a "sit-in" protest instead.
"About 567 NUM members are being held hostage by alleged AMCU members," NUM spokesman Livhuwani Mammburu told AFP.
The miners in Springs, east of Johannesburg, were supposed to come back to the surface on Monday morning after a night shift but failed to do so.
They include almost 70 women, some aged over 60, Mammburu said.
The dispute revolves around union representation at the mine, where NUM is currently the only group officially registered.
The AMCU says an overwhelming majority of miners have signed up to join it but it is yet to be given an official representation -- which it says is the reason for the protest.
"Workers can only come out once they are given the organisational rights," AMCU's regional secretary Tladi Mokwena told AFP.
Police spokeswoman Dimakatso Nevhuhulwi said officers were "on standby" and monitoring the situation while talks between the mine and the unions were ongoing.
"The police can confirm that approximately 550 mine employees are reportedly held hostage underground at a mine in Springs since Sunday," she added.
NUM said the company sent medics and a security team with food supplies to the miners but they have also been kept underground.
"It is distressing to learn that the crisis shows no signs of abating, and law enforcement appears to be absent in effectively addressing the ongoing hostage situation," said Ashor Sarupen, a lawmaker with the Democratic Alliance, South Africa's leading opposition party.
NUM was founded in 1982 by the country's President Cyril Ramaphosa, a former labour unionist. It remains the southern African nation's biggest mineworker union