A man was killed during a joint Army-Assam Rifles operation in Churachandpur's Henglep subdivision on Tuesday.
Police said he was a suspected militant and claimed an AK-47 rifle, ammunition and explosives were recovered from the site.
A BJP MLA and Kuki civil society groups disputed the police version, alleging the deceased was a civilian and demanding an independent inquiry.
A man was killed during a security operation in Manipur's Churachandpur district on Tuesday, with police identifying him as a 'suspected militant', while a BJP MLA and local Kuki civil society groups alleged that the deceased was an unarmed civilian and demanded an independent inquiry into the incident.
According to a statement issued by Manipur Police on Wednesday, the encounter took place in the Henglep subdivision of Churachandpur district during an operation conducted by a joint team of the Assam Rifles and the Army.
"The encounter occurred between militant groups and the security forces. During the exchange of fire, one suspected militant was killed," the statement said.
Police said an AK-47 rifle, magazines, ammunition, explosives and other incriminating materials were recovered from the site. A case has been registered and further investigation is underway.
However, the official account has been challenged by local leaders and civil society organisations in the area.
In a statement, BJP MLA Letzamang Haokip, who represents Henglep Assembly constituency, condemned the incident and alleged that "a civilian has lost his life at the hands of those entrusted with his protection". He called for a judicial and independent inquiry to establish the facts surrounding the killing.
Separately, the Joint Kuki Civil Society Organisations (CSOs) identified the deceased as Lenminsang Haokip, a resident of Songkong village, and alleged that he was not a militant.
The organisations claimed that security forces had subjected the village to drone and mortar bombardment during the operation. According to their statement, Lenminsang remained at home due to health reasons while other villagers had gone to work in nearby jhum fields. They alleged that after a drone strike occurred near the village, he ran out of his house in search of safety and was subsequently chased and shot dead by security personnel.
The CSOs further alleged that security forces took away the body after the incident and that it had not been returned to the family at the time of issuing their statement. They also claimed that blood-stained clothing and footwear believed to belong to the deceased were recovered near his residence.
Describing the incident as a possible "fake encounter", the organisations demanded accountability from the security personnel involved and called for justice for the deceased and his family.
Earlier this month, three Kuki villagers, including a woman, were killed and several houses were torched in Kangpokpi district, triggering fresh tensions in the hill districts. Days later, two members of the Kuki community were killed in separate attacks, while the bodies of six Naga men who had been abducted weeks earlier were recovered, underscoring the deteriorating security situation and the growing cycle of retaliatory violence involving Kuki and Naga groups.
