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He was found unconscious in his flat in Kochi after an overdose of sleeping pills.
Senior advocate Shyam Divan, appearing for the PFI, agreed with the court's view that the organisation should have first approached the high court and then come to the top court.
The journalist, who was jailed for over two years while attempting to report a gangrape and murder case in Uttar Pradesh, spoke in Kannur on Saturday.
The PFI challenged the order passed by the UAPA Tribunal affirming the Centre's decision to declare it as an 'unlawful association'.
The city police has lodged cases against the two under anti-terror law Unlawful Activities (Prevention) Act (UAPA) for allegedly receiving money to spread pro-China propaganda.
Purkayastha and Chakravarty were arrested by the Special Cell of the Delhi Police on Tuesday. Police have sealed the NewsClick's office in Delhi.
Delhi Police's Special Cell searched 30 locations of NewsClick and its journalists in a case filed under the UAPA following allegations that it received money for pro-China propaganda.
Khalid had sought bail on grounds that he neither had any criminal role in the Delhi violence nor any "conspiratorial connect" with any other accused in the case.
A bench of Justices Aniruddha Bose and Bela M Trivedi said the matter needs to heard on a non-miscellaneous day.
Khalid's petition challenging the October 18 last year order of the Delhi High Court, which had rejected his bail plea in the matter, came up for hearing before a bench of Justices A S Bopanna and Prashant Kumar Mishra.