It said yesterday an employee was fatally injured on Friday following a drilling incident.
"Authorities and organised labour were immediately informed and an investigation into the incident is currently underway," Harmony said.
Operations in the affected section were suspended in the interim.
CEO Peter Steenkamp said executives and management extended their sincerest condolences to family, friends and colleagues.
"The company will ensure that the necessary support is provided to the family in dealing with this tragedy," he said.
The mine has a workforce of more than 4,800 people.
South Africa had last year recorded the lowest number of mining fatalities on record of 51 but recently exceeded this number year-to-date.
Kusasalethu contributed 8% to Harmony's production in the year to June 30, before Harmony acquired AngloGold Ashanti's assets in South Africa.
Harmony had reiterated its aim for zero harm in its latest annual report, where it recorded six fatalities for the year to June 30.
Harmony shares (JSE: HAR) closed down 0.45% yesterday to R71.05, valuing it at R43.77 billion (US$3 billion).