Philippine National Police Chief Alan Purisima said Senior Superintendent Valeriano de Leon was relieved of his duties following the incident Sunday.
Police initially reported the 13 victims were hired guns, but family members of the men have denied the accusation.
GMA News said one of the victims was an environmentalist while at least two others were policemen on active duty.
GMA News said the men were killed after they allegedly ignored a required border check near the town of Atimonan, prompting the gunfire.
Interior Secretary Manuel "Mar" Roxas said 15 investigative operatives at the checkpoint were in civilian clothes and a portion of the officers involved are "deemed in restrictive custody."
Roxas said the police have until Friday to submit a complete report on the incident.