The incident occurred at its Kusasalethu mine during maintenance.
"I can confirm that the fire has occurred but the fire has now been contained," spokeswoman Marian van der Walt said.
Kusasalethu, a deep level operation west of Johannesburg, is Harmony's single largest gold producer.
Samuel Dlamini, a National Union of Mineworkers official, told Reuters that hundreds of miners who were underground when the fire began were put in a safety chamber and that emergency rescue teams had been sent to retrieve them.
Last year [DATA HAR:Harmony] closed Kusasalethu for two weeks to try to remove illegal miners who had been trespassing on the operation and were believed to be starting fires.
The company said in statement that 287 of the 486 workers were safely in the underground refuge bays and that mine rescue teams were trying to locate the other workers.