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The company said on Thursday an employee had succumbed to his injuries, following a winch-related incident on January 22 at its Phakisa mine in the Free State province.
Harmony had reported a fatality due to a fall of ground incident at Bambanani, also in Free State, mid-month.
"We are once again reminded that - despite the various safety initiatives that have been embedded throughout the company - we need to do even more to ensure that our work areas are safe," CEO Peter Steenkamp said.
"It is for that reason that a safety day has been declared throughout Harmony, aimed at reinforcing Harmony's safety standards and safe behaviour."
The company said organised labour and relative authorities had been informed and an investigation into the Phakisa incident was underway.
Steenkamp extended his condolences and Harmony said it would support the family with the bereavement process and counselling.
The company had reported nine fatalities at its South Africa mines in 2020, with none recorded at its operations in Papua New Guinea.
The Association of Mineworkers and Construction Union had said in January it hoped 2021 would "not be a terrible safety year like 2020 was".
South Africa had surpassed 2019's record low number of 51 mining fatalities by early December.