Lesotho's foreign ministry reported the incident to Pretoria, it said.
The DMRE said an investigation into the incident with the help of Harmony Gold - the previous owner of the mine which ceased operations in the 1990s - determined that methane levels were very high in the ventilation shaft and an explosion had occurred.
"As such, it is currently too risky to dispatch a search team to the shaft. However, we are considering various options to speedily deal with the situation," it said.
A spokesperson for mining and energy minister Gwede Mantashe said it might take a while to retrieve the bodies as authorities did not want to risk losing more lives.
Harmony said it viewed the incident - which occurred in the third week of May - as a criminal matter and has handed it over to the South African police for further investigation.
"We were informed by one of the illegal miners (who survived) that there had been an explosion and that the incident resulted in loss of life," said Jared Coetzer, Harmony's head of investor relations.
Coetzer said the shaft was acquired in the mid-1980s but was closed shortly after due to a methane gas explosion and was never used by the miner.
"We don't know how the people got to the place where the explosion occurred," he added.
Methane is a highly explosive greenhouse gas often found in underground mines and poses serious safety and health threats to mine workers.
Talks were ongoing between South Africa and Lesotho to retrieve the bodies and bring them home, said Thapelo Mabote, a government spokesperson for the small mountain kingdom.
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