Thalassery Principal Sessions Judge V K Anilkumar allowed the agency's plea, seeking custody of Jayarajan for questioning in the case.
The court said that CBI could question Jayarajan on March 9, 10 and 11 and that only an investigation officer should be present at that time of questioning which should be carried out between 9 AM to 6 PM.
Jayarajan is now under treatment in Kozhikode Medical College.
CBI had in January listed Jayarajan as 25th accused and framed charges against him under the Unlawful Activities (Prevention) Act in connection with the case.