The company said the fatality had been caused by a groundfall incident, with investigations underway.
At least six fatalities have been recorded at Harmony mines since January.
The department of mineral resources said entities, including the Mine Health and Safety Council, were conducting research into seismicity and how its detection could be improved.
It urged companies to put safety first.
"The primary responsibility to ensure a safe working environment rests with the employer; employees also have a right to refuse to work in dangerous conditions. The department will continue to enforce compliance, in line with provisions in the mine health and safety act," the DMR said.
The National Union of Mineworkers (NUM) said it was "highly concerned" at the rate of fatal incidents taking place in the mining industry, saying it was "highly unacceptable" that over 45 mineworkers had already died so far this year.
"The NUM reiterates its call that there is a need to amend the mine health and safety act so that those who are found to be responsible for fatalities in the mining industry must be arrested, prosecuted and sent to jail. The mining bosses who are found to be negligent must be held accountable for all the accidents," it said.
The NUM and the Association of Mineworkers and Construction Union have called for minister of mineral resources Gwede Mantashe and president Cyril Ramaphosa to strengthen section 23 of the act to give more power to workers and unions.
Fellow miner Sibanye-Stillwater is facing a class action lawsuit in the US on behalf of shareholders to recover losses after 21 mine fatalities triggered a sharp fall in the company's share price.
Harmony's share price dropped Tuesday after the news to R22.37 (US$1.66) per share, but had gained 1.11% Wednesday to R22.70/share.