Chaudhry Nisar Ali Khan's warning came as Christians gathered for a prayer service to remember of a Taliban massacre at a school that left 132 children dead.
"We are receiving intelligence from across the country that the militants are getting ready for another savage and inhuman counter attack. All of us need to be on the alert," the minister said.
There have been a number of brutal attacks on Christians in Pakistan recently.
The attack on the school was not thought to be directly aimed at Christianity, though.
Speaking to Reuters Babar Masih, a local Christian, said: "As human beings we have been so greatly saddened by this incident that we do not have the words to describe our grief.
"The children who were killed were angels; they have awakened people by their sacrifice."