Shujaat Bukhari was shot by unidentified gunmen as he left his office in Srinagar, the disputed region's main city. Bukhari had boarded the vehicle and was leaving when he was shot repeatedly from a close range.
His driver and personal security officer (PSO) were also injured.
In 1991, editor of Alsafa Mohammed Shaban Vakil was killed by the Hizb-ul-Mujahideen.
The 49-page report - the first ever issued by the United Nations on the human rights situation in Indian-Administered and Pakistan-Administered Kashmir - details human rights violations and abuses on both sides of the Line of Control, and highlights a situation of chronic impunity for violations committed by security forces.
More than 130 people have been killed this year in militant violence in Kashmir.
Jammu and Kashmir Governor N N Vohra has conveyed shock and grief on the gruesome killing of Bukhari.
The three militants were caught on a CCTV camera, the police said.
"I'm anguished to hear about the killing of Shujaat Bukhari, editor of Rising Kashmir".
Relatives and friends of the Editor of"Rising Kashmir Shujaat Bukhari who was shot dead Thursday evening
Bukhari was the editor of Kashmiri newspaper Rising Kashmir.
Her political rival and former chief minister Omar Abdullah was equally devastated, putting out a series of tweets expressing his anguish. Senior militant leaders had criticised Bukhari and other Kashmiris involved in the proceedings.
Shujaat Bukhaari was the Editor-in-Chief of Srinagar-based newspaper, Rising Kashmir, and was known as a courageous and outspoken voice for justice and equality. "My deepest condolences to his family".
Union Home Minister Rajnath Singh termed it an "act of cowardice".
Speaking to ANI, Iftikhar Gilani, a senior journalist and a friend of Bukhari, said, "I had a conversation with him just 20 minutes before the incident".
Known for encouraging young and budding journalists in Kashmir, Bukhari, an avid social media user, would often talk about the threat to Kashmir journalism in a conflict situation.
Bukhari, who was in his 50's, was assigned security guards after he faced an assassination attempt in 2000. The Guild also calls upon the state and central government to enhance security for all journalists in Jammu and Kashmir.
Journalist Nidhi Razdan tweeted, "Devastating news". He said it was Tan attack on freedom of press and needs to be condemned in the strongest possible words.
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