President Cyril Ramaphosa has suspended the NPA's Nomgcobo Jiba and Lawrence Mrwebi pending the outcome of an inquiry into their fitness for office.
Jiba is the Deputy National Director of Public Prosecutions and Mrwebi the Special Director of Public Prosecutions.
The announcement was made on Thursday afternoon. The inquiry will be led by former justice of the Constitutional Court Yvonne Mokgoro.
In a letter to Jiba and Mrwebi Ramaphosa said: "I have taken into account the serious nature of allegations that you are unfit to be in so high an office, where the work of our criminal justice system is central to the critical and pressing matter of all prosecutions, especially prosecution of corruption cases and safeguard of our public purse.
"You hold a senior position with influence over a large swathe of the NPA. It is the interest of the NPA’s image as a whole that I consider here, and of the integrity of an enquiry (sic) that must result in the clearest and most convincing conclusions about the integrity, and sound leadership of the NPA."