It's Harmony's third fatality reported so far this year, following a scraper winch-related incident at Kusasalethu in February and a mud rush-related fatality at Tshepong in January.
Harmony said the Moab Khotsong employee was reported missing at the end of the day shift on Tuesday and an intensive search was begun.
CEO Peter Steenkamp committed Harmony's full support and cooperation to the official investigation and extended his personal condolences, and those of the company, to family, colleagues and friends.
"We are reinforcing across our operations the key elements of our safety journey - leadership, risk management and attainment of a proactive safety culture," Mr Steenkamp said.
Harmony acquired Moab Khotsong from AngloGold Ashanti in March 2018 and it was the company's second largest gold operation in 2019, with a grade of 8.17g/t.
The mine has a workforce of about 6,500 people and produced 5,646kg of gold in the nine months to March 31, of the company's total 30,814kg for the period.
The economic reef horizons are mined between 1,791m and 3,052m below surface.
South Africa's underground mines were allowed to ramp back up to 100% this week as the country further eased COVID-19 restrictions but Steenkamp said last week it would probably take about a month to return to full production.
Harmony's shares closed 11.1% lower yesterday to 5,181c, capitalising it at R27.7 billion (US$1.6 billion).
