Jesse Duarte has not resigned from the presidency, a spokesperson said on Sunday.
"She is still part and parcel of the hard-working team in the office of the President," said presidency spokesperson Zizi Kodwa.
The Sunday Times reported that Duarte on Thursday wrote African National Congress (ANC) secretary-general Gwede Mantashe an "emotional email" announcing her resignation.
She is currently the chief operations officer in the presidency.
Duarte had clashed with top Zuma aide and deputy director-general in the presidency, Lakela Kaunda, the paper reported.
"There aren't fall-outs. They're working together as one team. It does not mean a tension or a conflict," said Kodwa.
Confrontation happens in any working environment, he said.
"The report was meant to create suspicion and mistrust," said Kodwa.
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