The letter was also sent to the Chief Justice of Allahabad High Court, Chief Secretary, DGP and other officers of Uttar Pradesh.
The letter alleged that the family of the rape survivor was being threatened.
The Court asked the secretary General to submit a report as to why the letter written by the rape survivor was not placed before him.
Supreme Court on Thursday will hear the matter on judicial side.
The observations came when senior lawyer V Giri, who is assisting the court as an amicus curiae in child rape cases, sought urgent listing of the Unnao rape case.
The court also asked the Uttar Pradesh authorities to file a status report by Thursday on the accident of the Unnao rape case victim.