Fifty-three-year-old Bukhari, the editor of English daily 'Rising Kashmir', was shot dead soon after he boarded his car from his office located at Press Enclave in the heart of the city centre -- Lal Chowk.
Two of his personal security officers (PSOs) were also killed in the attack by terrorists.
The Foreign Office said Bukhari was known for carrying out his professional responsibilities with courage and conviction.
"There can be no justification for anyone to commit such brutality, which cannot be condemned enough," it said.
Praying for Bukhari's soul to rest in eternal peace, the Foreign Office said: "Our profound thoughts and prayers are with his family at this difficult time."
"May the Almighty Allah grant them the strength and fortitude to bear this irreparable loss," it said.
Bukhari, survived by his wife and one son and a daughter, was instrumental in organising several conferences for peace in the Kashmir Valley.
He was also part of the Track II process with Pakistan.
The unidentified militants, believed to be three in number, were waiting as it is believed that they had the knowledge about the time Bukhari was to leave office.
They fired indiscriminately on the vehicle carrying him and fled on a motorcycle along with a weapon of a PSO, Abdul Hamid, who was also killed on the spot.
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