The Commission for Gender Equality will continue with the Harris Commission despite staff members withdrawing their cooperation with the probe.
CGE staff say they want suspended chief executive Chana Majake reinstated and are withdrawing from investigations against her.
Majake was suspended in April after staff wrote a memorandum complaining about her.
An investigation led by Peter Harris was instituted to probe claims that Majake had "employed staff members without following procedures, and that she finalised a policy document and gazetted it without proper consultation with all CGE stakeholders and staff".
Two weeks ago, staff decided to withdraw from the Harris Commission.
CGE spokesman Javu Baloyi said: "The CGE can confirm that such a memorandum was presented, though it does not represent the sentiments of all CGE employees.
"The Harris Commission continues its investigation. We are confident that the commission will make objective findings."
Baloyi said Majake would remain suspended until the investigation into her conduct has been concluded.