Two Hizbul Mujahideen militants, including an reportedly M.Phil degree holder, were killed in an encounter with security forces in Nowgam area of the city on Wednesday.
The slain militants have been identified as Sabzar Ahmad Sofi and Asif Ahmad, an official said.
According to media reports, Sofi was pursuing PhD in Botany from Jamia Millia Islamia New Delhi, and had joined the militant ranks in the aftermath of killing of Hizbul Mujahideen commander Burhan Wani in July 2016.
However, Jamia Millia Islamia, in a statement, denied Sofi was a former research student of its university.
"No such student by the name of Sabzar Ahmad Sofi has ever been on the roll of the university or registered as research student. Moreover, we do not have any Botany department in the University," the statement said.
Sofia, in his early 30's, is the third highly educated person to have been killed this year after joining militancy.
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Earlier this month, AMU scholar turned militant Manaan Bashir Wani was killed in an encounter with security forces in north Kashmir Kupwara district while an assistant professor from Kashmir University Mohammad Rafi Bhat was killed in a gunfight in Shopian district two days after joining the militant ranks in May this year.
There has been an increasing trend of well educated youth joining militancy in recent years.
Esa Fazli, a engineering graduate from Ghulam Shah Badshah University, was killed in a gun battle earlier this year as well.
After Fazli's joining, an MBA student Junaid Ashraf Sehrai, son of Tehreek-e-Hurriyat Chairman Mohammad Ashraf Sehrai, also disappeared to join the militant groups.
"The standard operating procedures were followed during the operation and there was no collateral damage during the encounter," the official added.
Acting on a tip off about presence of militants in Suthu Kothair locality of Nowgam, security forces launched a cordon and search operation in the early hours, a police official said.
He said the militants opened fire on security forces during the search operation, triggering a gunbattle in which two ultras were killed.
Incriminating material besides arms and ammunition were recovered from the encounter site, he added.
Clashes broke out between protestors and security forces soon after the encounter ended, he said, adding the law enforcing agencies were engaged in pitched battles with the stone pelters for most part of the day.
Authorities snapped mobile Internet services in the city and shut educational institutions as a precautionary measure.