The encounter had taken place in Shopian's Amshipora area.
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While addressing a press conference in Srinagar, Kumar said further investigations were going on in this case.
"We have received the DNA sample results of three families of Rajouri and they have matched with those killed in Amshipora Shopian," he said.
Imtiyaz Ahmad, Abrar Ahmad, and Mohammad Ibrar from Rajouri district were killed by the security forces during the operation.
Earlier Army had said that an internal inquiry into the encounter killing of three persons in Shopian district of Jammu and Kashmir in July has held that the concerned security personnel had exceeded their powers under the AFSPA and recommended disciplinary proceedings.