Medupi power station manager Rudi van der Wal has resigned, Eskom confirmed on Monday afternoon.
Spokesperson for the power utility Dikatso Mothae said the resignation was unrelated to the current electricity supply challenges, which saw the return of load shedding last week.
According to Mothae, he tendered his resignation prior to the recent spate of load shedding, and will be taking up another job abroad. A handover is underway, she said.
Eskom reintroduced load shedding due to a shortage of capacity that followed the failure of a conveyor belt supplying Medupi power station in Limpopo with coal.
In addition, five electricity generating units are unavailable due to boiler tube leaks.
The conveyer belt at Medupi will be repaired by end of the week, Eskom said.
Earlier, energy analyst Chris Yelland tweeted that Van der Wal had been force to step down, something Eskom has denied.
On Sunday, the power generator communicated that supply constrained, stating that no outages were expected on Monday and the probability of load shedding was low for the week.
The company also said it had replenished diesel reserves for the open cycle gas turbines and to increase water levels at its pumped storage schemes in preparation for the week ahead.
President Cyril Ramaphosa has weighed in on the impact of power cuts, saying they "contributes to investor unease at a time when we are trying to attract more domestic and foreign capital to South Africa and to improve our global rankings on ease of doing business".