"Police did everything they could … but people [the miners] said they were not leaving and are prepared to fight," he said in an interview with Talk Radio 702 on Friday morning.
The minister said that "many" more were injured.
The North West health department confirmed earlier 25 people were killed in Thursday's bloody clash between miners and police at the mine in Rustenburg.
"The death toll is standing on 25," provincial health spokesperson Tebogo Lekgethwane told the South African Press Association on Friday. He said no injured people had been admitted to hospital.
No violence was reported there overnight after the shooting erupted when police sought to disperse armed, striking workers who had gathered on a hill in the area that had already seen 10 deaths in violent protests the past week.
It is still unclear who fired the first shots.
Police on Friday would not confirm the report from the health department which said 25 bodies had been removed from the scene and taken to the Phokeng Forensic Mortuary.
"The figure of the dead will only be released by the National Police Commissioner Riah Phiyega at the media briefing," said Captain Dennis Adriao.
Facts were not to be had at Lonmin's Marikana platinum mine on Thursday night, and even rumour was hard to come by; no official police spokespeople were answering phones, police on the scene were tight-lipped, medical workers knew little and shared less, and the local community had either barricaded itself or were in no-go areas.
At a nearby hospital, men with gunshot wounds to the legs were hastily treated before being removed by ambulance or, in at least one case, helicopter. No police were among those treated, one staff member said, but in the confusion that could not be confirmed.
At the scene of the shooting, at least seven bodies could be seen, in a single clump near the koppie where striking workers had been gathering all week. Forensic specialists confirmed that they were working on at least one other scene, suggesting that the death toll was higher, though perhaps not quite as high as the 28 that one witness claimed.
By midnight, police forensic teams were still combing the scenes for bullet casings and planting evidence flags in the veld. They would provide no detail on their work, except to indicate that they anticipated spending many more hours trying to independently piece together the sequence of events that had led to the deaths.
Had they found any evidence that police had been fired on before returning fire?
Like their counterparts from other branches of the service, they would say nothing. Nor was police commissioner Riah Phiyega anywhere to be found, though a statement said she was on the scene to assess it for herself.
By midnight, however, police activity indicated that no further trouble was expected, at least not immediately. Police units from as far afield as Krugersdorp, making up the team of several hundred police scattered about the mine, withdrew, leaving the crime scene largely unguarded and only perfunctory patrols in armoured vehicles active in the nearby settlement. Police would not say whether they would return in the morning.
Phiyega has been scheduled to give a press conference on Friday at her offices only a few kilometres from the scene of the shooting. – Additional reporting by Sapa