A bench of justices J Chelameswar and Abhay Manohar Sapre asked state authorities including the Director General of Police to "take necessary steps to shift the undertrial prisoner" from jail number one of Central jail at Hissar within two weeks.
The court has also issued notice to the Chief Secretary and the concerned Jail Superintendent.
Senior advocate Indira Jaising, appearing for the mother of the inmate, said this was a "serious" matter in which the jail superintendent had molested the girl inside the prison and alleged that moreover, he had criminal antecedents.
The girl is in jail in a case registered in connection with violent protests and clashes at self-styled godman Rampal Maharaj's ashram at Hissar in Haryana.
The plea was filed after the mother of the undertrial met her daughter in jail and got a letter which had the account of the incident.
"The act of the respondent no. 3 (jail superintendent) is in grave violation of provisions of the Punjab Jail Manual. The Chapter II defining Aims & Objectives of the jail administration wherein requisite protection and security of female prisoners has been laid to be duty of State where only female staff have access. Surprisingly, the respondent no. 3 had access to female prisons," the plea said.