The National Union of Mineworkers (NUM), one of the two unions involved, said 107 of the more than 500 workers who had failed to emerge from the Gold One mine in Springs, east of Johannesburg, after a night shift on Monday morning "have come back to the surface."
"They are currently at the medical station for further check-ups," NUM spokesman Livhuwani Mammburu told AFP.
NUM and management at the mine had alleged the workers were being "held hostage" by members of the Association of Mineworkers and Construction Union (AMCU), a rival union.
AMCU denied the allegations saying the miners were staging a "sit-in" protest.
But on Wednesday police said that some of the 107 who "made their way to the surface" confirmed in interviews with detectives "that they were indeed held against their will."
"I am told that they overpowered those that were holding them hostage and ran away," the NUM's Mammburu said of those who made it out.
Police spokeswoman Brenda Muridili said about 15 people were holding the miners captive, but in interviews with local media declined to say whether the captors belonged to a specific union.
Two paramedics and a security officer were among those still underground, she said.
- AMCU seeks recognition -
Earlier, the AMCU's regional secretary Tladi Mokwena contended all the miners were coming out "willingly" having run out of food.
"Management has closed all the routes for them to receive food. So, we couldn't allow workers to stay underground without food," he said.
An AFP reporter at the scene on Tuesday evening said police and security forces patrolled the area as about 100 miners, mostly from the AMCU, sang protest songs as they waited for the outcome of the meeting between the mine management and unions.
The dispute revolves around union representation at the mine, where the 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 official representation, which it says is the reason for the protest.
The NUM was founded in 1982 by the country's President Cyril Ramaphosa, a former labour unionist. It remains the nation's biggest mineworker union.
Some miners "have since been released to go home," police said, adding that they would "remain on site until the situation has been resolved."