Footage of the performance at a competition in Mthatha, in the Eastern Cape, emerged earlier this week, showing the girls dancing on stage, their breasts and buttocks exposed.
The video was taken during a segment about Xhosa tradition, the South African website TimesLive reports.
The matter has since been escalated to Ms Motshekga's national department.
"It is completely inappropriate on the part of educators and they should know better than to expose teenage girls to this form exploitation," the AFP news agency quotes her as saying in a statement.
"There is absolutely nothing wrong with being proud of your culture and heritage, but there was absolutely no need for these children to perform completely naked.
"That indignity goes against the values of our cultures."