"We have initiated an independent investigation," spokesperson Phumla Sekhonyane told Sapa on Tuesday.
She did not provide further information.
The Star reported that a Grade 8 history teacher allegedly told her class last Thursday that the reason government was failing was because it was led by black people.
A 13-year-old girl sent an SMS to her mother saying the teacher was out of hand after telling the class black people were stupid for voting for the African National Congress and that in the Western Cape people were "more than happy" with the Democratic Alliance, "thanks to white people", according to the newspaper.
According to the report, more parents were expected to complain.
The school said its governing body would make a statement in due course.