Johannesburg - Regional magistrate Stanley Gumede has been formally charged with misconduct by the Magistrate's Commission, City Press reported on Sunday.
Gumede was believed to be President Jacob Zuma's first choice to lead the National Prosecuting Authority (NPA).
He was served with the charges on Wednesday, according to the report.
Commission secretary Danie Schoeman told the newspaper on Friday that Gumede would remain at work while the probe was conducted.
According to City Press, presidential spokesman Mac Maharaj said the matter of appointing heads for the NPA and the Special Investigating Unit (SIU) was under consideration by Zuma.
The NPA has been without a permanent head since December 2011.
The Democratic Alliance reportedly said it would go to court if Zuma appointed Gumede.
In October, the Constitutional Court found that Zuma's appointment of former national director of public prosecutions (NDPP) Menzi Simelane was unconstitutional and invalid.
The Ginwala Commission of Inquiry into the fitness to hold office of Simelane's predecessor Vusi Pikoli had raised concerns about Simelane's understanding of the relationship between the justice department and the NPA.
At the time, Constitutional Court Judge Zac Yacoob said Simelane had been evaluated in terms of the Ginwala Inquiry.
Pikoli told City Press a new head was desperately needed to restore the NPA's dignity.
“The two biggest problems are a lack of leadership and political pressure, which is glaring,” he was quoted as saying.
“This person needs to be strongly independent, impartial and must not buckle under undue political pressure.” - Sapa