The duo were planning targeted killings in various north Indian states on the directions of Khalistan movement leaders sponsored by Pakistan's Inter-Services Intelligence, they said.
They were identified as Makhan Singh Gill alias Amli and Davinder Singh alias Happy, both residents of Noorpur Jattan village in Hoshiarpur, Punjab Director General of Police Dinkar Gupta said.
The home ministry said these individuals are operating from Pakistan and other foreign soil and involved in various acts of terrorism.
Khalistan Liberation Force chief Harminder Singh 'Mintoo' who along with five others escaped from the high security jail in Nabha on Sunday, was arrested by Punjab Police after he was deported from Thailand in November 2014.