Minister of Women, Children and People with Disabilities Lulu Xingwana has been accused of using her position to forcibly remove her nephew's two-year-old daughter from her mother, the Daily Dispatch reported on Friday.
The toddler's parents had been involved in a custody battle.
The mother, who cannot be named to protect the identity of the child, claimed that she and other relatives were manhandled by Xingwana's bodyguards.
However, Xingwana, through her spokesperson Cornelius Monama, this week denied the allegations, according to the report.
"The court found it was in the best interest of the child to be taken to Pretoria by her father where she would continue with her early childhood development," Monama said in an email.
"The minister was there [in court] to support a relative.
"There is nothing wrong for the minister to be accompanied by her protectors."
According to the mother, the case was set down to be heard in the Mthatha High Court last Friday. She did not attend after her lawyer reportedly told her he would ask for a postponement.
However, a provisional order was granted that the child be taken to Pretoria immediately and placed in the custody of the father.
The mother was also ordered to give reasons why the order should not be granted before 1 March.
The report added that Xingwana's entourage had arrived at the mother's Upper Ngqwarha home in a state vehicle and that the normal procedures for handing over a child during such a dispute involved counselling.