Chief executive Emma-Jane Cross said some girls in very rough schools were pushed into sex acts for protection.
But other anti-bullying groups and teachers' unions challenged the charity to provide evidence of this.
The warning comes as the House of Commons Education Select Committee published a report highlighting weaknesses in the way schools tackled bullying.
Speaking after the report was published Ms Cross called for an urgent government investigation into the "sexual exploitation of young people by young people".
But her charity's claims were questioned by the National Union of Teachers, which said it had no evidence that this sort of behaviour was happening in schools.
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