The CPI(M) Politburo said the CBI made a "deliberate effort" to target Jayarajan, the party's Kannur district secretary.
Kannur, the home turf of Kerala Chief Minister Pinarayi Vijayan, has been a hotbed of clashes between workers of the RSS-BJP combine and the CPI(M).
"The Politburo strongly opposes the use of the UAPA to file charges against Jayarajan. This is gross misuse of its provisions and a deliberate effort to target a political leader," it said in a statement.
It charged him under the stringent law for the killing, which it described as a "terrorist act".
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