Bukhari was shot outside his office in the commercial hub of the region's main city of Srinagar.
Waseem Ahmad, a local journalist, told Reuters that he heard gunfire ringing out and, reaching the location, found Bukhari and his two guards lying in a pool of blood in their auto. Two police officers provided to him by local authorities for his security were also killed in the evening attack, according to S.P. Vaid, the region's police chief.
He was well-known in Kashmir and was previously a correspondent for the Indian newspaper The Hindu.
Senior Superintendent of Police (SSP) Srinagar, Imtiyaz Ismail Parray, said that the police have procured the CCTV footage and the role of militants in the killing was being investigated. "While paying his condolences to the bereaved family has prayed for the eternal peace to Shujaat Bukhari", the statement said.
This is the first attack on a journalist in a long time in Kashmir which has been facing severe attacks on civilians and security personnel in the recent past.
Bukhari described the threat to Kashmiri journalists in a 2016 article for BBC News.
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"An attack on a journalist challenges the very foundations of a free press and vibrant democracy and more so in a state like Jammu and Kashmir that is going through militancy. He would often fight for the issues of people through his columns and various discussions but alas this voice of people stands silenced today brutally", she added in her message.
Amongst those who took part in the last rites of the journalist and visited his ancestral home to condole with the family were Opposition leader Omar Abdullah and Ministers from the PDP-BJP government.
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".
Omar Abdullah, who had expressed his condolences on Thursday rushed to Bukhari's house on Friday morning to pay his last respects. "That Shujaat's colleagues were able to bring out the paper in the face of insurmountable grief is a testament to their professionalism & the most fitting tribute to their late boss", the former Chief Minister wrote on Twitter while sharing a picture of the front page of the paper.
Chief Minister Mehbooba Mufti expressed shock at the killing.
The killing has sent shockwaves across the journalistic fraternity. All anti-India forces are attacking journalist. The Guild also calls upon the state and central government to enhance security for all journalists in Jammu and Kashmir. It was even condemned by Pakistan and Kashmiri separatists.