Raza Mahmood Khan, convener of Aghaz-i-Dosti, went missing on Saturday, his colleague Raheemul Haq said.
"We last met Raza on Saturday evening for an open discussion on extremism specifically focusing on the recent Islamabad sit-in of Islamists," he said.
Raza is also associated with another community initiative that brings people together for dialogues and debates on issues critical to building a peaceful society.
Raza's brother Hamid Nasir has submitted an application to Naseerabad police for an FIR but the case has not been registered yet.
The sit-in ended on November 27 after military brokered a deal between the protesters and the PML-N government.