The incident took place this morning and additional security forces including the Army, Manipur police and Assam Rifles have rushed to Khoupum.
A search operation was launched to nab the militants, the police added.
NSCN(I-M) had signed the Framework Agreement on the longstanding Naga problem on August 3, 2015 with the Centre. It had signed a ceasefire with the Centre in 1997 which was extended indefinitely in 2007.
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