Jayarajan, the party's Kannur district secretary who had been summoned by CBI in connection with the probe, was arraigned as the 25th accused in the case relating to the murder of RSS worker E Manoj in September 2014, allegedly by a group of CPI-M workers.
Cases under Unlawful Activities (Prevention) Act and a conspiracy charged have been slapped against him, counsel for Jayarajan said.
Reacting to the development, CPI(M) politbureau member Pinarayi Vijayan, who is now undertaking a political yatra criss-crosing the state, told reporters here that the party would face the case "politically and legally".
CPI(M) state secretary Kodiyeri Balakrishnan alleged the case against Jayarajan was only to "appease BJP and RSS."
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Soon after his anticipatory bail plea was turned down, Jayarajan had got himself admitted to the Pariyaram Medical College and is undergoing treatment for heart ailment.
42-year-old Manoj, 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.