The deaths occurred in the ventilation shaft at an abandoned site in the gold mining town of Welkom, 260km from Johannesburg, the Department of Mineral Resources and Energy (DMRE) said.
"We are receiving reports that other suspected illegal miners have assisted in retrieving in at least three bodies, so 28 are believed to still be underground," DMRE spokesman Ernest Mulibana told AFP.
The fatalities are believed to be illegal miners who had come from neighboring Lesotho, a tiny kingdom completely surrounded by South Africa, it said.
The deaths possibly happened on May 18, although the cause remains unknown.
A search team has not been dispatched to the shaft for safety reasons, Mulibana said.
"Given the high levels of methane, it is currently risky for anyone to go down," he said.
Lesotho's foreign ministry alerted South Africa's High Commission in Maseru on June 10, but the incident was only announced by Pretoria in an overnight statement on Thursday. The reason for the delay was unknown.
The mine was previously owned by Harmony Gold Mining Company, one of South Africa's largest producers. It stopped operations in the 1990s.
Thousands of unregistered miners known as "zama zamas" operate in South Africa, scavenging obsolete mines for gold. The conditions are arduous and often perilous.
"Although this is a unique and strange situation," a joint effort will "ensure that the suspected deceased illegal miners are brought to the surface," the DMRE said.