Mohafe on Thursday left Rise and Shine, who also recently parted ways with goalkeeper coach Modiri Marumo.
According to a source close to City, management are discussing Molekwa's fate and are rumoured to be considering bringing in an European coach next season.
"Phuti Mohafe is gone now after Marumo," says the informant.
"The club is still finalising the issue of the technical team and is expected to make announcements very soon."
Meanwhile, the Absa Premiership side are expected to part ways with Donald Mokondelela at the end of the month, having only signed the ex-Orlando Pirates midfielder on a three-year deal in August.