Brigadier Anura Gunawardena was arrested following investigations conducted by the CID over the incident.
Last month three soldiers were also arrested over the shooting incident.
Violence erupted during a protest by residents of Rathupaswala on August 01, 2013 as security forces and protesters clashed in Weliweriya, resulting in the death of three persons and injuring over 30.
Human rights groups had condemned the crackdown against the protest by villagers who were demanding clean drinking water for thousands of residents of Weliweriya and have criticised the manner in which authorities had handled the situation.
The Sri Lanka Human Rights Council (SLHRC) in 2013 submitted a report on the Rathupaswala incident claiming that the murders were committed by the alleged open air firing at protesters by the Army.
They also recommended the military to investigate into the matter and bring the criminals to book. (Colombo Gazette)