Justice Minister Michael Masutha will lead the task team.
This followed the cabinet’s decision to back Parliament’s inquiry into Molefe’s reappointment.
Public Enterprises Minister Lynne Brown also announced on Thursday an investigation into Eskom, stretching to 2007, when load shedding began.
The task team set up by Zuma will include Masutha, Finance Minister Malusi Gigaba, Energy Minister Mmamoloko Kubayi and Brown.
Opposition parties said they would see Molefe in court on Tuesday to explain why he should be kept in the position of chief executive at the power utility.
“Cabinet is concerned about the recent developments at Eskom. It appreciates that the matter regarding the re-employment of Mr Brian Molefe as the chief executive of Eskom is before courts and in Parliament, and shall therefore respect these processes,” said acting government spokesperson Phumla Williams.
The intervention of Zuma came after Brown said she would launch her own investigation into Eskom.
Natasha Mazzone of the DA said the power utility was in crisis because Brown had failed in her oversight responsibilities.
The full-scale inquiry into Brown’s reappointment of Molefe would get to the bottom of the issues, she added.
Thembinkosi Rawula of the EFF said Brown had endorsed Molefe’s decision to resign from Eskom.