The gunfight had started on Tuesday and ended late last evening.
The police have confirmed that all the three JeM militants hiding in Nazneenpora village of Tral area have been killed by the security forces.
The slain militants include one Pakistan national and two locals.
"Five security personnel including on CRPF (Central Reserve Police Force) jawan and four army soldiers have been injured in this encounter," the police said.
Following specific information about three militants hiding in Nazneenpora village of Tral area, troops of Rashtriya Rifles, CRPF and Special Operations Group (SOG) of the Jammu & Kashmir Police surrounded the village.
As the security forces tightened the cordon around hiding militants, they fired at the security forces triggering a gunfight that ended with the killing of the three JeM militants.
This was the first anti-militancy operation in J&K after the Bharatiya Janata party withdrew support from the Jammu and Kashmir Peoples Democratic Party (PDP)-led coalition government headed by Mehbooba Mufti.
The state has been placed under Governor's rule which as per the J&K constitution can last for three months.