A report by the auditor general on the Passenger Railways Agency of South Africa’s finances for 2014.
The danger in not reporting it, Madonsela added, was that victims could end up being blamed for the rape instead of their attackers.
"I know of several people who were raped and one involved a boy who was 10 years older than the girl. It was not reported and in this instance, the young girl was blamed even though she was only seven years old," Madonsela said.
She also called for a "responsive" justice system to help rape victims and encourage others to come forward and report the incidents.
"Saying no to rape as a society also means making sure that when it happens everyone plays a role in reporting it and that the criminal justice system is responsive."
In October, a woman who was gang-raped as a 14-year-old and subsequently made to wait nine years for justice as the case was postponed more than 40 times, received only R50,000 as compensation from the Department of Justice and Constitutional Development.
The payout followed a recommendation in 2010 by Madonsela that the department apologise and compensate the woman and her family.
Commenting on the matter, Madonsela congratulated the Justice Department for seeing to it that the rapist was charged.
Madonsela also called on fathers to be better role models for their sons to ensure that they grow up to be responsible men in the society.
Despite the country's high rate of child rapes, Madonsela remained hopeful that eventually, it would change.
"I think the message is getting through and there is high level of consciousness.
"A rapist is a sick person ... clearly a grown man can't see a 2-year-old or a 10-year-old as a woman or even a sexual figure.
"We need risk management and to find those men at risk and act on it," she said.