Captain Bhoopinder Singh is currently in the custody of the Army, with informed sources saying he may face Court Martial proceedings.
Havildar A K Tomar succumbed to injuries at Army's 92 Base Hospital here. Tomar had sustained grievous injuries during a gunfight with militants in Kanigam area of Shopian on Friday.
Shopian 'fake' encounter: Jammu and Kashmir police files chargesheet against Army officer, two others
The 1,400-page chargesheet was filed in the court of principal district and sessions judge, Shopian on Saturday by the head of the Special Investigation Team (SIT), the officials said.
A police official said the identity and group affiliation of the slain militant was being ascertained.
The Court of Inquiry, which completed its probe earlier in September, had found "prima facie" evidence that troops had "exceeded" powers during the encounter.
Security forces launched a cordon and search operation in Kutpora area of south Kashmir's Shopian district following specific information about the presence of militants there.
Security forces launched a cordon and search operation at Melhura in Zainapora area of Shopian on Monday evening following information about presence of militants in the area.
Security forces launched a cordon and search operation in the Chakura area of Shopian following information about the presence of militants there
They said the role of the three civilians including a person who had allegedly led the army to the youths in Amshipura in Shopian needs to be thoroughly examined by the police.
Mohammad Yousuf, the father of 25-year-old Mohammad Ibrar, said the government has fulfilled one of their demands of exhuming the bodies and handing them over to their families for proper burial.
Security forces launched a search operation at Sugan village in Zainapora area following information about the presence of militants there
Officials said the families of the three men were called from Rajouri district in Jammu region and taken to the spot where the trio was buried.
The DNA samples of the three labourers — Imtiyaz Ahmed, Abrar Ahmed and Mohammad Ibrar — matched with their family members in Rajouri.
Kashmir politicians seek action to make the case a deterrent in future
On July 18, the Army had claimed three militants were killed in Amshipura village in the higher reaches of south Kashmir's Shopian district.