Public Protector Busisiwe Mkhwebane, a constitutionally mandated anti-graft official, was appointed in 2016 by Ramaphosa's predecessor Jacob Zuma. She is seen as allied to Zuma's faction within the ruling African National Congress (ANC) party, which is opposed to Ramaphosa's faction, a claim she has denied.
Her tenure has been marred by allegations she drove an anti-Ramaphosa campaign and she has been widely criticised for losing several high-profile court judgements.
The development comes after the president asked Mkhwebane in March to provide him with reasons not to suspend her, after a parliamentary committee decided to continue with its motion to remove her.
On Wednesday, a statement issued by the Public Protector said Mkhwebane had received unfair criticism and has also been accused by the media and politicians of "targeting" certain members of the executive branch of government and getting involved in party politics.
The South African parliament had in 2020 begun proceedings to oust her amid criticism of her record in office.
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