Some 447 gold miners were held below ground east of Johannesburg in a near repeat of a three-day protest in October, the Gold One company said.
A small group of balaclava-wearing employees was behind the "hostage situation" that began at the start of Thursday's night shift, said Ziyaad Hassam, head of legal at the Gold One mine in Springs, Gauteng province.
The rebels had taken control of the miners' security access cards "so they are not able to get out from underground," Hassam said.
Police were monitoring events but had not immediately seen criminal activities, a spokeswoman said.
Those held included some middle managers and contractors, the company said. Two miners who managed to escape early Friday confirmed the events to the management.
More than 500 miners were trapped underground for almost three days at the same mine in October during a standoff between rival labor unions.
Hassam said the reasons for the new incident were not immediately clear but the company suspected a link to disciplinary hearings over the previous incident.
Fifty workers were dismissed after hearings ended on Thursday, he said.
A company investigator involved in the disciplinary process was murdered this week, Hassam added, without giving details.
Police told South African media that the 55-year-old man was shot dead in his car on Tuesday but have not said what the motive was.
Separately, 250 miners demanding better wages entered the third day of an underground protest at the Bakubung platinum mine west of Pretoria but media reports said an accord had been reached to end the action.
The National Union of Mineworkers, NUM, said the workers wanted higher wages and better benefits.
NUM spokesman Livhuwani Mammburu said workers were also angry that the operators wanted to cut 500 jobs but were hiring new managers.
Some 28 miners suffering from chronic illnesses came to the surface on Thursday and Friday.
Local ENCA television said that following talks between the NUM and mine managers, 100 workers had decided to come up and the rest would soon follow.
The ministry of mineral resources said it was deeply concerned at the "growing trend" of underground protests.
"This poses a serious health and safety risk that could result in injuries and loss of life," ministry spokesman Makhosonke Buthelezi told AFP.
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