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The principal of a primary school outside Thohoyandou was handed the letter of suspension while at school.
The suspension came barely a day after he was granted R10,000 bail by the Vuwani Magistrate's Court on Tuesday.
"Yes, we can now confirm that the department has suspended (the principal). We have handed him a letter of precautionary suspension with effect from March 1," said department spokesman Pat Kgomo.
Kgomo said the principal was suspended with full pay and that he could be dismissed from the teaching profession if investigations proved that he had had sex with the victim.
The department said last week that five teachers in the province were suspended for sexual offences involving female pupils between 2010 and 2011.
The decision by the department to suspend the principal was applauded by the Commission for Gender Equality and the SA Council of Educators.