The young Zuma, whose appointment sparked an outcry from citizens and opposition parties, resigned from her position in December.
Thuthukile notified the department of her intentions to leave in August, and it was accepted by minister Siyabonga Cwele.
She has been replaced by Frans Mthombeni.
Department spokesman Siyabonga Qoza confirmed Thuthukile was no longer in the employ of the ministry.
"She left in December last year," Qoza said. "She had communicated her intentions to leave in the middle of the year before leaving in December."
He said there was an agreement on the hand over period between Thuthukile and her successor.
When asked why the department did not announce her departure, Qoza revealed that government made announcements or statements only on the appointment of director-generals and deputy director-generals.
Presidential spokesman Bongani Majola refused to comment.
He referred all questions to Thuthukile, who could not be reached for comment.
Thuthukile is the youngest of Zuma's four daughters with his ex-wife African Union Chairperson Nkosazana Dlamini-Zuma.
She holds an Honours degree in Anthropology from Wits University