The three were nabbed from a hide out at Virajpet in Karnataka, police said.
Two CPI(M) workers have been already been arrested in connection with the killing even as the Congress alleged that they were not the real culprits.
Congress-led UDF Opposition in Kerala had demanded a CBI probe into the killing of the Youth Congress functionary.
Senior Congress leader, K Sudhakaran, who was staging a huger strike here for the last five days demanding the arrest of the real culprits behind the killing, had also stated yesterday that he would continue the stir till the government order a CBI investigation in the case.