The encounter took place when personnel of Assam Rifles 43rd battalion rushed to Changoubung village under Kangpokpi sub-division late last night following reports of movement some armed militants, the reports said.
In the heavy exchange of fire that ensued the militant identified as Paohulen Kipgen, younger brother of former Manipur minister Haokholet Kipgen, was killed.
One self-loading rifle, one pistol and a few rounds of ammunition were recovered from the possession of the deceased, the reports said.
Kipgen's family denied the official reports and claimed he was picked up from his village home by Assam Rifles personnel posted at nearby Kangpokpi when he was supervising the construction of a house yesterday.
Haokholet Kipgen said if his brother, who has been staying at the house with other family members was a militant then why did Assam Rifles personnel not arrest him and hand him to police station as per the provisions of Armed Forces special Powers Act, 1958 in vogue in the state.
Claiming that his brother was an innocent civilian, the former minister said he would lodge a formal complaint with the authorities and the police and urge the government to take appropriate action.