According to Release International, Pastor Judoon had been supporting a Christian accused of blasphemy.
The pastor went missing after he left his house at 6.00pm on Sunday. Police later found his bag and motorbike several miles away.
Pastor Judoon is a village elder of Kamahan outside of Lahore.
The village is just miles from where another Christian pastor, Babu Shahbaz, was arrested after being accused of writing his name on a Qur'an and ripping up its pages, despite his illiteracy.
Pakistan has some of the world's strictest blasphemy laws. Those found guilty of blaspheming against Islam and the prophet Muhammad face the death penalty.