Workers began the wildcat strike at the mine west of Johannesburg on March 23.
Approximately seven to 10 days of gold production have been lost at a rate of 15kg of gold production per day, the firm said.
The strike had been encouraged by the Association of Mineworkers and Construction Union (Amcu) in response to disciplinary procedures against 40 employees following an illegal sit-in at Kusasalethu in January.
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Harmony said the Amcu and its members had ignored the court order granted on Friday, with no employees reporting for work over the weekend or on Monday.
“An ultimatum has now been issued to Kusasalethu employees to return to work tomorrow night, failing which they may be subject to disciplinary action,” the gold producer said.