Jayarajan, Kannur district secretary, who was summoned by the police for questioning, was arrested soon after his arrival at the SP's office and taken to a Magistrate Court.
He has been charged with IPC section 118 (concealing design to commit offence punishable with death or imprisonment for life).
Abdul Shukkoor, an activist of the Muslim Youth League (IUML) was murdered allegedly by CPI-M activists at Keezhara near Kannavam in the district in February this year.
Police claimed that some of the prominent CPI(M) leaders in the district were aware of the circumstances of the murder and they had sought to harbour the culprits.
Jayarajan was accompanied by party functionaries and a large number of CPI(M) workers when he arrived at the office of the SP, who called him for the second time for questioning.
According to police sources, Jayarajan was arrested after interrogation of party functionaries, including CPI(M) MLA T V Rajesh.
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Jayarajan, however, dubbed the charge as "fabricated and politically motivated".
Talking to reporters before appearing before the police team, he alleged "anti-CPI(M) elements" in the police and a section of media had been spreading canard against the party.