A bench of Justices A K Goel and U U Lalit asked Khetan to approach the Delhi High Court with his plea in which he has also sought framing of guidelines to be adopted by the probe agencies for dealing with such complaints.
The AAP leader had approached the apex court on May 24 and sought protection alleging threats.
He said that on May 9, he had received a threatening letter written in Hindi at his office claiming that his death was imminent.
Mr Khetan had said he had even complained to the Delhi Police Commissioner about the threat but no substantive action has been taken by them till now.
"It is submitted that the language and content of this letter is similar to the threatening article published by Sanatan Prabhat against Dr Narendra Dabholkar, both before and after he was killed. The threat is a chilling reminder of the growing confidence of the anti-national and fascist forces who want to exterminate all dissenting voices with silence," he said.
Mr Khetan, who is the vice chairman of Dialogue and Development Commission of Delhi, had sought a ban on rightwing organisation, Sanatan Sanstha, and a CBI probe monitored by the apex court into the alleged death threats.
He had also sought police protection following the alleged threats from several right-wing outfits and formulation of guidelines for protection of people who get death threats.
"The petitioner herein respectfully submits that there are right-wing extremist organisations active in the country today. Some of the prominent groups among them are Sanatan Sanstha, Abhinav Bharat, Hindu Janjagruti Samiti, Hindi Rakshak Samiti, Bajrang Dal, Durga Vahini, Sri Ram Sene and Vishwa Hindu Parishad.
"Such radical right-wing extremist organisations have notably in the last couple of years carried out several murderous attacks on those who do not share their ideology and those who are rationalists, secularists, free thinkers, anti-superstition and critical thinkers," the plea said.