Captain Johannes Ramphora said the miners shot at security guards who confronted them at the site, east of Johannesburg. Security guards shot back, wounding one miner.
Authorities said explosives also were found in the shaft.
"We arrest these illegal miners, but you find after a week there are other new people there," Capt Ramphora said. "It's a very difficult situation for police, but we are trying."
He said it was the third major mine raid in the last two years. In August, security guards shot and killed four illegal miners at the same shaft.
Aurora Empowerment Systems, which owns the mine, is in a pay dispute with the miners they inherited when they bought several mines from a bankrupt company.
Illegal miners often stay in shafts for months at a time. The dangers can include cave-ins as well as noxious fumes or explosions