According to the company, the miners have been trespassing into the operation and are believed to be starting fires.
A spokeswoman for Harmony said the operation would involve the police and mine security.
"No production will occur during this period and employees will be sent on leave," Harmony said in a statement.
"Management has decided to take serious action to tackle illegal mining at its Kusasalethu mine. The initiative has been stepped up following the outbreak of a fire at the mine yesterday afternoon, which is believed to have been caused by illegal miners," the statement said.
The fire was the third at Kusasalethu, a deep level operation west of Johannesburg, this month. No one has been hurt in the fires.
Harmony has been battling to get Kusasalethu back to full production 20 months after reopening the operation, which had shut for several weeks at the start of 2013 because of labour violence rooted in a union rivalry.
"Kusasalethu’s production has not reached planned levels and these ongoing incidents of sabotage further undermine the mine’s sustainability," the Harmony statement said.
"Although illegal mining is more common at abandoned and near-surface mines, it is still rife in deep-level underground mines where trespassers illegally enter the mines with the intent of mining and removing gold or copper bearing material."
The company also said its employees had been threatened by illegal miners, while others had provided them with assistance in entering the mine as well as food and water.
"During October 2014, 105 illegal miners have been arrested and about 25 employees are subject to disciplinary action."