Operations at Harmony Gold's Doornkop mine will cease until the area has been declared safe for employees, Minister Susan Shabangu said on Thursday.
This came after eight miners were found dead following an underground fire at the mine west of Johannesburg.
No worker would be allowed on site and in areas affected by the incident, Shabangu told the media after a briefing by mine management on the incident.
"Once the last remaining employee has been found and the fire has been brought under control, we will then begin with an inquiry in terms of the Mine Health and Safety Act, to find out what led to this incident," said Shabangu.
The department's inspectors, led by the Chief Inspector of Mines, have been on site since the day of the incident.
Shabangu expressed her condolences to the families of the deceased, as well as management and co-workers at Harmony's Doornkop mine.
"The incident is a lesson for us all. The gold industry has over the past five years improved its health and safety standards tremendously, and for such an incident to occur is obviously a setback," Shabangu said.
"As the Regulator, we must look at what happened and learn from it to ensure we can, as far as possible, prevent it in future," she concluded.
Nine workers were unaccounted for after a fire broke out on Tuesday night in a stope adjacent to 192 level haulage (some 1, 733m underground), following a seismic event that triggered a fall of ground.
Rescue workers have located the bodies of eight miners, and the search continued for the ninth employee.
The fire has been subdued, but rescue work was hampered by smoke and a fall of ground, the company said.
On Wednesday, eight other miners were rescued from the underground refuge bay and were unharmed, said the company.
The incident is the most serious in South African mines since nine workers died in a rock fall at a platinum mine in July 2009.
Mining fatalities declined from 123 in 2011 to 112 in 2012, the lowest ever recorded, but that figure is still totally unacceptable, the Congress of South African Trade Unions said.