A bench headed by Justice A K Patnaik sent the case back to the high court for taking a fresh look at it.
The court passed the order on an appeal filed by the State of Kerala challenging the acquittal of the accused in the case.
The Kerala High Court had acquitted 35 persons who were convicted by a special court in September 2000.
The girl from Suryanelli in Idukki district of Kerala was abducted in January 1996 and was transported from place to place across Kerala.
The apex court on January 3, this year had decided to hear the appeal against the acquittal of the 35 accused in the gangrape case on an urgent basis within three weeks.
The bench had given the assurance after it was brought to its notice that the appeal against the high court verdict had been pending in the apex court for the last eight years.