A bench of Justices N V Ramana and P C Pant also directed P Krishnadas, the Chairman of Nehru Group of Institutions, to remain in Coimbatore in Tamil Nadu, from where his office functions, until the case proceedings are over.
The apex court, however, denied the state government's request to cancel bail and grant custody of Krishnadas for interrogation, as the case has been transferred to the CBI.
The top court was hearing a plea of the state government challenging the Kerala High Court order granting bail to accused Krishnadas and college vice-principal N K Sakthivel, who have been charged with abetment to suicide.
Pranoy, an 18-year-old student of Nehru Engineering College at Pambady in Thrissur, was found hanging in his hostel bathroom on January 6 this year.
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Sakthivel, examination supervisor C P Praveen, and another staff Sibin are also accused in the case.
It was alleged that the authorities had threatened Jishnu after he organised protests against certain decisions of the college management.
Krishnadas was arrested on April 4 but later released on bail.