The encounter took place when personnel of Assam Rifles 43rd battalion rushed to Changoubung village under Kangpokpi sub-division late last night following inputs of movement of some armed militants, the reports said.
In the heavy exchange of fire, 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, however, denied such 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.
"Why did Assam Rifles personnel not arrest my brother and hand him to the police as per the provisions of Armed Forces Special Powers Act, 1958, if he was a militant?" Haokholet Kipgen asked.
His brother was an innocent civilian, Kipgen said, adding that he would lodge a formal complaint with the authorities and the police and request the government to take appropriate action.