Correctional Services spokesman Manelisi Wolela has denied allegations that student leader Mcebo Dla.
A widower is on the run after impregnating his 16-year-old daughter and learning that the police were searching for him.
The girl told the police her father first attempted to rape her before her mother's death last year.
And though she was afraid to report the attack, she opened up after teachers at her school near Komatipoort realised her behaviour had changed.
"My dad eventually raped me shortly after my mom's death last year. He has subjected me to rape on several occasions and I was afraid to tell anyone about this matter until lately," said the girl who cannot be identified because she is a rape victim.
She said the rapes happened in her bedroom where her father would wake her up during the night.
The girl said her teachers were the first to realise something was wrong with her and when they challenged her, she told all about the rapes.
Her father used to work at the TSB sugar cane farm until his disappearance.
The girl confessed that it was too much for her to be pregnant at her age, but explained it was even worse when her biological father was the culprit
Tonga police spokesman Constable Mzwandile Nyambi confirmed that cases of rape and incest were being probed at the station.
l In a similar but separate incident, a 52-year-old man was arrested last year after he allegedly raped and impregnated his own daughter.
The victim is staying at the nearby Sikhwahlane Trust.
The suspect was denied bail during his last appearance before the Tonga magistrate's court last year.
He denied the charges against him when Sowetan confronted him at the time and is expected to appear in the magistrate's court soon.