This is the first arrest after CBI took over the case on the request of the state government.
The arrested were identified as Sini, Riju and Biju, all stated to be local leaders of CPI(M).
42-year old Manoj, a district functionary of RSS, was hacked to death in politically-volatile Kathiroor by an unidentified gang.
RSS-BJP leaders alleged CPI(M) was behind the killing which occurred on a day when BJP President Amit Shah was in Thiruvananthapuram on a visit to the state.
The state government had decided to hand over the case to CBI on the basis of a report from state police chief K S Balasubramanian who did not rule out the possibility of the murder having inter-state and even foreign links.