Thalassery District and Sessions court Judge V K Anil Kumar rejected the bail petition of Jayarajan, who was arraigned as the 25th accused in the case connected with the murder of RSS activist E Manoj in September 2014.
CBI had early this month listed Jayarajan, Kannur District Seretary of the party and framed charges against him under the Unlawful Activities (Prevention) Act in connection with the case.
This the third time that the court has dismissed the anticipatory bail plea of the Marxist strongman.
CPI-M state leadership has all along maintained that the case was politically motivated and was part a "conspiracy" hatched by RSS and Congress in the state.
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Jayarajan, who was admitted to a hospital soon after his bail plea was rejected on January 19, continues to remain in the hospital.
Manoj (42), a district functionary of RSS, was hacked to death in politically-volatile Kathiroor in Kannur district on September 1, 2014 allegedly by a group of CPI-M workers.
CBI informed the court today that they wanted Jayarajan in custody for 24-hours for questioning.
The agency, which took over the probe in the case, had filed a charge sheet against 19 accused in the Thalassery court in March last year.
Manoj was an accused in a case related to an unsuccessful attempt on Jayarajan's life in 1999.