Senior CPM leader P Jayarajan was arrested on Wednesday in connection with the murder of Indian Union Muslim League (IUML) activist Abdul Shukoor.
Soon after, violence broke out in many parts of Kannur and the party called a statewide bandh on Thursday.
Central teams will be deployed in the area as a precautionary measure.
The arrest of the Kannur district secretary comes as the party is reeling under senior leader MM Mani's accusation that it lists and executes political opponents.
The accusation came on the heels of the brutal murder of rebel TP Chandrasekharan.
The murder of Shukoor, 21, took place in February after he allegedly orchestrated an attack on Jayarajan's car near Thaliparambha.
He and his friend Zachariah, 23, were caught by CPM workers after their roles were verified with the help of an MMS made during the attack. They were given a "trial" at a "kangaroo court".
Following the "trial", they were hacked with hatchets and knives in the presence of over 100 witnesses, said a police officer. Shukoor died, Zachariah escaped with injuries.
The police said there was enough evidence to arrest Jayarajan.
After Shukoor's murder, police had arrested 22 CPM workers.
One of them, Sumesh, had told police that order to kill Shukoor and his friend came from Thaliparambha co-operative hospital, where Jayarajan had been admitted with minor injuries.
The conspiracy was hatched in presence of senior CPM leaders and later, they sheltered most of the accused, the officer said.
Condemning the arrest of his aide, party state secretary Pinarayi Vijayan said it was part of a larger conspiracy to implicate senior leaders in murder cases and weaken the party. "The Oommen Chandy government is playing with fire," he said.