The suspects are Army intelligence unit’s Lt. Col. Kumara Ratanayake, Lt. Col. Siriwardena, Staff Sergeant Rajapakse and Corporal Jayalath.
Previously, a Sergeant Major and two Tamils, ex-LTTE spies later turned military informants, had been arrested and interrogated.
They had given information leading to the latest arrests.
CID investigations have uncovered details of several crimes that had taken place during the war, say police headquarters sources.
The probe into Ekneligoda’s disappearance was halted during the general election period on the orders of the prime minister following intelligence warnings that arrests of military officials could lead to turmoil in the Army.