A civilian was also killed by stray bullet yesterday during law and order problem.
"Three holed up terrorists eliminated; bodies of two terrorists & three weapons recovered," Army's Northern Command said in a tweet.
Army officials at Srinagar-based 15 Corps Headquarters, however, refused to comment on the operation.
A police official said two bodies were recovered from the debris of the house where the ultras were hiding.
The slain militants were both locals and identified as Majid Mohiuddin Zargar of Qoimoh in neighbouring Kulgam district and Ruhul Amin Dar of Vessu in Anantnag district.
He said one of the bodies was severely burnt.
One army jawan was injured in the gunfight that began in the early hours yesterday.
The security forces had cordoned off the area on Wednesday evening following information about presence of Lashkar-e-Toiba militants there.
A 24-year-old man was killed allegedly after being hit by a "stray bullet" near the site of encounter.
Arif Shah, a resident of Sangam area of Anantnag district, was hit by the "stray bullet" when security forces were dealing with a group which was indulging in stone-pelting near the encounter site, the official said.
They also claimed that several other persons were injured in the clashes between protesters and security forces.
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