“I wish to officially confirm that Dr Loyiso Mbabane has resigned as the DG of the province with effect from 31 January 2015 following developments regarding legal processes surrounding him,” Phumulo Masualle said in a statement.
Masualle commended Mbabane for putting the interests of the provincial government and premier’s office ahead of his own.
Acting DG Mahlubandile Qwase would fill the position in the interim.
Times Live reported on Monday that Mbabane, who started his job on January 5, is accused of raping a relative in 2005, when she was 15, and again on January 22.
He was arrested in the parking area at his office the next day.
Last week, East London Magistrate Merwin Meyer denied Mbabane bail on the grounds that he might interfere with witnesses, the website reported.
His trial is set for March 25.