The 40-year-old JCO, identified as Konsam Kheda Singh, was on leave at his home in Charangpat when suspected armed persons overpowered him and whisked him away.
Police said a massive manhunt has been launched in Thoubal and nearby areas.
A high alert has been sounded on the Imphal - Moreh National Highway.
Police and security personnel were searching for the JCO by stopping vehicles.
(With UNI inputs)