A police spokesman in Srinagar said militants barged into the house of Mohammad Aslam Awan, and fired indiscriminately at the inmates, killing Awan and his three-year-old son identified as Arif Ahmad Awan instantly.
He said the bodies of the two victims were taken to sub-district hospital in Keller for autopsy.
Police has registered a case and started investigations.
The state chief minister, Omar Abdullah on Thursday denounced the killings and challenged the separatist leaders 'over their silence on the incident.'
The killings follow the grenade attack at a camp of the special operations group at Imam Sahib in Shopian early this week, killing two cops including a police sub-inspector identified as Sethi Ram.
Police has been conducting searches and raids to nab those involved in the attack.
Shopian district has been on the boil ever since the rape and murder of two young women whose bodies were found by a village stream on May 30.