He was booked under IPC Section 153(a) (promoting enmity between groups) on a petition by Muhammed Siraj, district secretary of Students Federation of India, CPI(M)'s student wing, they said.
Kunmannon had posted on Facebook a video which he claimed was of CPI(M) activists celebrating the killing of RSS worker Choorakadu Biju at Payannur.
Biju was hacked to death at Payyanur town in Kannur, which has witnessed a series of clashes between ruling CPI(M) and the RSS for the past one year.
He was out on bail when he was killed.
The CPI(M) had rejected Rajasekharan's charge and alleged that the BJP leader was trying to add fuel to fire.
Yesterday, Chief Minister Pinarayi Vijayan had stated in the assembly that the government would register a case against Rajasekharan after examining the video and also that the BJP leader's claim was incorrect and illegal.